[Xperia Z3 Compact General] Amplifiction:
I was unable to get the removal tool to work. To be honest, I didn't know what to do with it. But I went through the entire procedure again, this time using XZDR 2.8.12 and firmware D5803_23.1.A.0.726_Generic RU.ftf. (Found here)

I now have working recovery. Thank you!

.690 and .726 are indeed both Lollipop, both 5.0.2. This indeed kept partial root. If I understand correctly, your update did change Android version numbers, which probably doesn't allow it to qualify as minor. Will refrain from performing Sony OTA updates in the future :)

The bad news: I still have partial root after running the entire procedure again:

GT Data Recovery still says so. (After receiving SuperSU permission)

Root Explore in ES File Explorer (restored from Google Play) still doesn't work. Asks for SU, but then gives error.

Probably related: SMS Backup and Restore is unable to write to external SD card.

Flashing RICDefeat in recovery gets me an error. Unable to install. "Status 7". Or in TWRP "Error executing updater binary in zip". Does anyone know what I can do about this?

I used the version of RICDefeat found in OP, couldn't find any newer on Google. Is anyone aware of a newer version?

Additional information: I think this problem manifested itself already while installing recovery.

Note: "mount: permission denied (are you root?)"

Also, "mkdir: can't create directory '/storage/sdcard1/XZDualRecovery': Read-only file system". (I am unsure if I had my SD card in at that time, though.) But that folder is there now!

==============================================
= =
= PhilZ Touch, CWM and TWRP Dual Recovery =
= Maintained by [NUT] =
= =
= For Many Sony Xperia Devices! =
= =
==============================================

1. Installation on ROM rooted with SuperSU
2. Installation on ROM rooted with SuperUser
3. Installation on unrooted ROM using the TowelRoot method
4. Install ADB drivers to windows
5. Exit

Please choose install action.
[1,2,3,4,5]?1
* daemon not running. starting it now on port 5037 *
* daemon started successfully *

=============================================
Waiting for Device, connect USB cable now...
=============================================
Device found!

=============================================
Getting ro.build.product
=============================================
Device model is D5803
Firmware is 23.0.A.2.93

=============================================
Step2 : Sending the recovery files.
=============================================
6 KB/s (31 bytes in 0.005s)
1767 KB/s (18103 bytes in 0.010s)
48 KB/s (501 bytes in 0.010s)
417 KB/s (11968 bytes in 0.028s)
2147 KB/s (65965 bytes in 0.030s)
143 KB/s (3082 bytes in 0.021s)
1280 KB/s (30148 bytes in 0.023s)
132 KB/s (1357 bytes in 0.010s)
3366 KB/s (34473 bytes in 0.010s)
106 KB/s (1089 bytes in 0.010s)
1658 KB/s (13592 bytes in 0.008s)
cannot stat 'disableric': No such file or directory
2509 KB/s (719520 bytes in 0.280s)
2352 KB/s (3112915 bytes in 1.292s)
2349 KB/s (2314025 bytes in 0.962s)
2391 KB/s (1934801 bytes in 0.790s)
668 KB/s (11641 bytes in 0.017s)

=============================================
Step3 : Setup of dual recovery.
=============================================
Look at your device and grant supersu access!
Press any key to continue AFTER granting root access.
-rwxr-xr-x 1 shell shell 719520 Apr 20 2015 /data/local/tmp/recover
y/busybox
Druk op een toets om door te gaan. . .
mkdir: can't create directory '/storage/sdcard1/XZDualRecovery': Read-only file
system
grep: /cache/XZDualRecovery/XZDR.prop: No such file or directory
grep: /cache/XZDualRecovery/XZDR.prop: No such file or directory

##########################################################
#
# Installing XZDR version 2.8.12 RELEASE
#
#####

Temporarily disabling the RIC service, remount rootfs and /system writable to al
low installation.
mount: permission denied (are you root?)
Remount of system failed, applying MohammadAG's wp_mod module solution now.
Module exists in system partition, loading it now.
This firmware does not require byeselinux, will not install it.
Copy recovery files to system.
Rename stock mr
Copy mr wrapper script to system.
Rename stock chargemon
Copy chargemon script to system.
Copy dualrecovery.sh to system.
Copy rickiller.sh to system.
Installing NDRUtils to system.
Creating /system/.XZDualRecovery to store a backup copy of busybox and the init.
rc files.
Copy busybox to system.
Copy init's *.rc files in to /system/.XZDualRecovery.
Trying to find and update the gpio-keys event node.
Found and will be using /dev/input/event3!
Trying to find and update the power key event node.
Found and will be monitoring /dev/input/event2!
Speeding up backups.
Make sure firstboot goes to recovery.

=============================================
DEVICE WILL NOW TRY A DATA SAFE REBOOT!
=============================================

=============================================
Your installation has already cleaned up after
itself if you see the install.bat/install.sh exit.
=============================================

=============================================
Installation finished. Enjoy the recoveries!
=============================================

Druk op een toets om door te gaan. . .

In case anyone is wondering, Giefroot gave me no errors:

==============================================
= =
= giefroot v3 =
= created by zxz0O0 =
= =
= Many thanks to: =
= - [NUT] =
= - MohammadAG =
= - Keen Team =
= =
==============================================

* server not running *
* daemon not running. starting it now on port 5037 *
* daemon started successfully *
=============================================
Waiting for Device, connect USB cable now...

Make sure that you authorize the connection
if you get any message on the phone
=============================================
Device found

=============================================
Sending files
=============================================
19 KB/s (259 bytes in 0.013s)
3099 KB/s (22220 bytes in 0.007s)
0 KB/s (237 bytes in 1.000s)
1327 KB/s (13592 bytes in 0.010s)
166 KB/s (1705 bytes in 0.010s)
3366 KB/s (34473 bytes in 0.010s)
2650 KB/s (4016989 bytes in 1.480s)
2214 KB/s (657704 bytes in 0.290s)
61 KB/s (752 bytes in 0.012s)
1728 KB/s (44259 bytes in 0.025s)
pkg: /data/local/tmp/exploitServiceApp.apk
Success

=============================================
Running exploit
Make sure you have enabled "Allow mock locations"
in Developer Settings
=============================================
Please wait for the device to reboot
Druk op een toets om door te gaan. . .

Done. You can now unplug your device.
Enjoy root
=============================================

What to do next?
- Donate to the people involved
- Install dualrecovery by [NUT]
- Backup TA partition

Druk op een toets om door te gaan. . .