[Xperia Z3 Compact Q&A, Help & Troubleshooting] MrBratka:
Hi, I got the same issue today. I could flash FTF this morning on my XPERIA Z1 (C6903) but can't flash other version ftf now.

23/052/2015 12:52:00 - INFO - Device connected in flash mode
23/052/2015 12:52:16 - INFO - Selected Bundle for Sony Xperia Z1 (C6903). FW release : 14.6.A.0.368. Customization : Customized DE
23/052/2015 12:52:16 - INFO - Preparing files for flashing
23/053/2015 12:53:00 - INFO - Please connect your device into flashmode.
23/053/2015 12:53:01 - INFO - Device disconnected
23/053/2015 12:53:19 - INFO - Device connected in flash mode
23/053/2015 12:53:20 - INFO - Opening device for R/W
23/053/2015 12:53:20 - INFO - Reading device information
23/053/2015 12:53:20 - INFO - Phone ready for flashmode operations.
23/053/2015 12:53:20 - INFO - Opening TA partition 2
23/053/2015 12:53:20 - INFO - Current device : C6903 - BH90B21E1F - 1277-0154_R2D - 1274-8313_14.5.A.0.270 - EURO-LTE_14.5.A.0.270
23/053/2015 12:53:20 - INFO - Closing TA partition
23/053/2015 12:53:20 - INFO - Start Flashing
23/053/2015 12:53:20 - INFO - Processing loader.sin
23/053/2015 12:53:20 - INFO - Checking header
23/053/2015 12:53:20 - INFO - Flashing data
23/053/2015 12:53:20 - INFO - Loader : S1_Root_6732 - Version : LOADER_RELEASE_MSM8974_32_AID_4 / Boot version : S1_Boot_MSM8974_Rhine1.3_LA1.04_11 / Bootloader status : ROOTABLE
23/053/2015 12:53:20 - INFO - Max packet size set to 512K
23/053/2015 12:53:21 - INFO - Making a TA backup
23/053/2015 12:53:21 - INFO - Opening TA partition 1
23/053/2015 12:53:21 - INFO - Start Dumping TA partition 1

Was waiting for one hour for progress but nothing changed.

Haven't found any solution yet. I hope someone had this sorted out and reply asap. My phone is working as it was before nothing have changed.

EDIT: I noticed it creates folders under flashtool directory "Flashtool\registeredDevices\BH90B21E1F\s1ta\2015-09-23_12-53-21" with one file in it "1.ta" which size is 0 bytes I don't think anything was happening meanwhile...

EDIT(SOLUTION): I Tried to uninstall the flashtool removed the leftover folders (just backed up firmwares folder which had my FTF's). Then installed again to default directory launched and tried to flash the same FTF as before. And voila it works (for me at least). Reply if it will work for you too. :)

---------- Post added at 11:30 AM ---------- Previous post was at 10:47 AM ----------

Here's my latest log which went succesfully. Flashtool didn't try to dump the TA partition for some reason now.

23/020/2015 14:20:32 - INFO - Selected Bundle for Sony Xperia Z1 (C6903). FW release : 14.6.A.0.368. Customization : Customized DE
23/020/2015 14:20:32 - INFO - Preparing files for flashing
23/021/2015 14:21:14 - INFO - Please connect your device into flashmode.
23/021/2015 14:21:39 - INFO - Device connected in flash mode
23/021/2015 14:21:39 - INFO - Opening device for R/W
23/021/2015 14:21:39 - INFO - Reading device information
23/021/2015 14:21:40 - INFO - Phone ready for flashmode operations.
23/021/2015 14:21:40 - INFO - Opening TA partition 2
23/021/2015 14:21:40 - INFO - Current device : C6903 - BH90B21E1F - 1277-0154_R2D - 1274-8313_14.5.A.0.270 - EURO-LTE_14.5.A.0.270
23/021/2015 14:21:40 - INFO - Closing TA partition
23/021/2015 14:21:40 - INFO - Start Flashing
23/021/2015 14:21:40 - INFO - Processing loader.sin
23/021/2015 14:21:40 - INFO - Checking header
23/021/2015 14:21:40 - INFO - Flashing data
23/021/2015 14:21:40 - INFO - Loader : S1_Root_6732 - Version : LOADER_RELEASE_MSM8974_32_AID_4 / Boot version : S1_Boot_MSM8974_Rhine1.3_LA1.04_11 / Bootloader status : ROOTABLE
23/021/2015 14:21:40 - INFO - Max packet size set to 512K
23/021/2015 14:21:41 - INFO - Parsing boot delivery
23/021/2015 14:21:49 - INFO - Found a template session. Using it : D:\Downloads\#Programs\$Android Utilities\XPERIA Z1-honami\Flashtool\devices\C69XX\default.fsc
23/021/2015 14:21:49 - INFO - Opening TA partition 2
23/021/2015 14:21:49 - INFO - Writing TA unit 00002774. Value : [01]
23/021/2015 14:21:49 - INFO - Closing TA partition
23/021/2015 14:21:49 - INFO - Processing partition.sin
23/021/2015 14:21:49 - INFO - Checking header
23/021/2015 14:21:49 - INFO - Flashing data
23/021/2015 14:21:49 - INFO - Opening TA partition 2
23/021/2015 14:21:49 - INFO - Processing dbi_S1_Boot_MSM8974_Rhine1.3.1_LA1.04_16_AID_4_S1-SDI2-6732-PID1-0004-SDI_S1-BOOT-6732-0004-MMC.sin
23/021/2015 14:21:49 - INFO - Checking header
23/021/2015 14:21:49 - INFO - Flashing data
23/021/2015 14:21:49 - INFO - Processing emmc_appsboot_S1_Boot_MSM8974_Rhine1.3.1_LA1.04_16_AID_4_PLATFORM-MSM8974-LIVE-HWID007B00E1-SWID09-OEM1-AID4-DEBUG00_S1-BOOT-6732-0004-MMC.sin
23/021/2015 14:21:49 - INFO - Checking header
23/021/2015 14:21:49 - INFO - Flashing data
23/021/2015 14:21:49 - INFO - Closing TA partition
23/021/2015 14:21:49 - INFO - Opening TA partition 2
23/021/2015 14:21:49 - INFO - Writing TA unit 0000084f. Value : [1A, CE, 28, 00, 01, 00, 06, 05, 00, 02, 02, 51, 00, 10, 03, 00, 02, 04, 02, 05, 00, 01, 03, 02, 00, 10, 05, 00, 03, 03, 05, 00, 10, 05, 00, 05, 83, 02, 00, 10, 02, 00, 05, 85, 0A, 00, 02, 00, A9, 09, BE, BA, A9, 09, 00, 00, 04, 00, 03, 00, 02, 00, 04, 00, 04, 00, B0, 04, 0E, 00, 06, 00, B8, 0B, 01, 4B, 00, 00, 00, 03, 96, 00, 2C, 01]
23/021/2015 14:21:49 - INFO - Writing TA unit 000008fd. Value : [00]
23/021/2015 14:21:49 - INFO - Closing TA partition
23/021/2015 14:21:49 - INFO - Opening TA partition 2
23/021/2015 14:21:49 - INFO - Processing s1sbl_S1_Boot_MSM8974_Rhine1.3.1_LA1.04_16_AID_4_PLATFORM-MSM8974-LIVE-HWID007B00E1-SWID65-OEM1-AID4-DEBUG00_S1-BOOT-6732-0004-MMC.sin
23/021/2015 14:21:49 - INFO - Checking header
23/021/2015 14:21:49 - INFO - Flashing data
23/021/2015 14:21:49 - INFO - Processing sbl1_S1_Boot_MSM8974_Rhine1.3.1_LA1.04_16_AID_4_PLATFORM-MSM8974-LIVE-HWID007B00E1-SWID00-OEM1-AID4-DEBUG00_S1-BOOT-6732-0004-MMC.sin
23/021/2015 14:21:49 - INFO - Checking header
23/021/2015 14:21:49 - INFO - Flashing data
23/021/2015 14:21:49 - INFO - Processing tz_S1_Boot_MSM8974_Rhine1.3.1_LA1.04_16_AID_4_PLATFORM-MSM8974-LIVE-HWID007B00E1-SWID07-OEM1-AID4-DEBUG00_S1-BOOT-6732-0004-MMC.sin
23/021/2015 14:21:49 - INFO - Checking header
23/021/2015 14:21:49 - INFO - Flashing data
23/021/2015 14:21:50 - INFO - Closing TA partition
23/021/2015 14:21:50 - INFO - Opening TA partition 2
23/021/2015 14:21:50 - INFO - Processing cache.sin
23/021/2015 14:21:50 - INFO - Checking header
23/021/2015 14:21:50 - INFO - Flashing data
23/021/2015 14:21:51 - WARN - apps_log is excluded from bundle
23/021/2015 14:21:51 - INFO - Processing kernel.sin
23/021/2015 14:21:51 - INFO - Checking header
23/021/2015 14:21:51 - INFO - Flashing data
23/021/2015 14:21:53 - INFO - Processing fotakernel.sin
23/021/2015 14:21:53 - INFO - Checking header
23/021/2015 14:21:53 - INFO - Flashing data
23/021/2015 14:21:55 - INFO - Processing rpm.sin
23/021/2015 14:21:55 - INFO - Checking header
23/021/2015 14:21:55 - INFO - Flashing data
23/021/2015 14:21:55 - INFO - Closing TA partition
23/021/2015 14:21:55 - INFO - Opening TA partition 2
23/021/2015 14:21:55 - WARN - userdata is excluded from bundle
23/021/2015 14:21:55 - INFO - Processing system.sin
23/021/2015 14:21:55 - INFO - Checking header
23/021/2015 14:21:55 - INFO - Flashing data
23/026/2015 14:26:49 - INFO - Processing amss_fs_1.sin
23/026/2015 14:26:49 - INFO - Checking header
23/026/2015 14:26:49 - INFO - Flashing data
23/026/2015 14:26:49 - INFO - Processing amss_fs_2.sin
23/026/2015 14:26:49 - INFO - Checking header
23/026/2015 14:26:49 - INFO - Flashing data
23/026/2015 14:26:49 - INFO - Processing amss_fsg.sin
23/026/2015 14:26:49 - INFO - Checking header
23/026/2015 14:26:49 - INFO - Flashing data
23/026/2015 14:26:49 - INFO - Closing TA partition
23/026/2015 14:26:49 - INFO - Opening TA partition 2
23/026/2015 14:26:50 - WARN - Unit 2404 not found in bundle
23/026/2015 14:26:50 - WARN - Unit 2212 not found in bundle
23/026/2015 14:26:50 - INFO - Closing TA partition
23/026/2015 14:26:50 - INFO - Opening TA partition 2
23/026/2015 14:26:50 - INFO - Closing TA partition
23/026/2015 14:26:50 - INFO - Opening TA partition 2
23/026/2015 14:26:50 - INFO - Processing elabel.sin
23/026/2015 14:26:50 - INFO - Checking header
23/026/2015 14:26:50 - INFO - Flashing data
23/026/2015 14:26:52 - INFO - Closing TA partition
23/026/2015 14:26:52 - INFO - Opening TA partition 2
23/026/2015 14:26:52 - INFO - Writing TA unit 00002725. Value : [32, 30, 31, 35, 2D, 30, 39, 2D, 32, 33, 20, 31, 34, 3A, 32, 36, 3A, 35, 32, 00]
23/026/2015 14:26:52 - INFO - Writing TA unit 00002774. Value : [00]
23/026/2015 14:26:52 - INFO - Closing TA partition
23/026/2015 14:26:52 - INFO - Ending flash session
23/026/2015 14:26:52 - INFO - Flashing finished.
23/026/2015 14:26:52 - INFO - Please unplug and start your phone
23/026/2015 14:26:52 - INFO - For flashtool, Unknown Sources and Debugging must be checked in phone settings