[Xposed Framework Modules] Roughy:
Unfortunately the logs do not indicate anything breaking horribly.

However, it does list the last 20-or-so transactions made to Exi's database:

Most recently executed operations:
0: [2018-05-27 15:46:35.437] [Pid:(0)]executeForCursorWindow took 0ms - succeeded, sql="PRAGMA database_list;"
1: [2018-05-27 15:46:35.436] [Pid:(0)]executeForLong took 0ms - succeeded, sql="PRAGMA page_size;"
2: [2018-05-27 15:46:35.436] [Pid:(0)]executeForLong took 1ms - succeeded, sql="PRAGMA page_count;"
3: [2018-05-27 15:46:33.487] [Pid:(10494)]executeForLastInsertedRowId took 1ms - succeeded, sql="INSERT INTO emoji_keyboard_panel_items_12(modifiers_supported,style,text,variants,type) VALUES (?,?,?,?,?)"
4: [2018-05-27 15:46:33.487] [Pid:(10494)]prepare took 0ms - succeeded, sql="INSERT INTO emoji_keyboard_panel_items_12(modifiers_supported,style,text,variants,type) VALUES (?,?,?,?,?)"
5: [2018-05-27 15:46:33.479] [Pid:(10494)]executeForLastInsertedRowId took 2ms - succeeded, sql="INSERT INTO emoji_keyboard_panel_items_12(modifiers_supported,style,text,variants,type) VALUES (?,?,?,?,?)"
6: [2018-05-27 15:46:33.479] [Pid:(10494)]prepare took 0ms - succeeded, sql="INSERT INTO emoji_keyboard_panel_items_12(modifiers_supported,style,text,variants,type) VALUES (?,?,?,?,?)"
7: [2018-05-27 15:46:33.471] [Pid:(10494)]executeForLastInsertedRowId took 3ms - succeeded, sql="INSERT INTO emoji_keyboard_panel_items_12(modifiers_supported,style,text,variants,type) VALUES (?,?,?,?,?)"
8: [2018-05-27 15:46:33.471] [Pid:(10494)]prepare took 0ms - succeeded, sql="INSERT INTO emoji_keyboard_panel_items_12(modifiers_supported,style,text,variants,type) VALUES (?,?,?,?,?)"
9: [2018-05-27 15:46:33.465] [Pid:(10494)]executeForLastInsertedRowId took 2ms - succeeded, sql="INSERT INTO emoji_keyboard_panel_items_12(modifiers_supported,style,text,variants,type) VALUES (?,?,?,?,?)"
10: [2018-05-27 15:46:33.465] [Pid:(10494)]prepare took 0ms - succeeded, sql="INSERT INTO emoji_keyboard_panel_items_12(modifiers_supported,style,text,variants,type) VALUES (?,?,?,?,?)"
11: [2018-05-27 15:46:33.452] [Pid:(10494)]executeForChangedRowCount took 4ms - succeeded, sql="DELETE FROM emoji_keyboard_panel_items_12"
12: [2018-05-27 15:46:33.451] [Pid:(10494)]prepare took 0ms - succeeded, sql="DELETE FROM emoji_keyboard_panel_items_12"
13: [2018-05-27 15:46:29.313] [Pid:(10494)]executeForCursorWindow took 0ms - succeeded, sql="SELECT * FROM emoji_keyboard_panel_items_13"
14: [2018-05-27 15:46:29.312] [Pid:(10494)]prepare took 0ms - succeeded, sql="SELECT * FROM emoji_keyboard_panel_items_13"
15: [2018-05-27 15:46:29.311] [Pid:(10494)]executeForCursorWindow took 0ms - succeeded, sql="SELECT * FROM emoji_keyboard_panel_items_12"
16: [2018-05-27 15:46:29.310] [Pid:(10494)]prepare took 0ms - succeeded, sql="SELECT * FROM emoji_keyboard_panel_items_12"
17: [2018-05-27 15:46:29.303] [Pid:(10494)]executeForCursorWindow took 2ms - succeeded, sql="SELECT * FROM emoji_keyboard_panel_items_11"
18: [2018-05-27 15:46:29.303] [Pid:(10494)]prepare took 0ms - succeeded, sql="SELECT * FROM emoji_keyboard_panel_items_11"
19: [2018-05-27 15:46:29.298] [Pid:(10494)]executeForCursorWindow took 1ms - succeeded, sql="SELECT * FROM emoji_keyboard_panel_items_10"

SELECT * FROM emoji_keyboard_panel_items_ ... here it is loading all the emoji panels, most certainly when you opened the keyboard.

Next up is INSERT INTO emoji_keyboard_panel_items_12 several times, which would be the emoji you clicked being inserted into the recent emoji table.

That's all looks fine and dandy, but what's weird is these two lines here:

13: [2018-05-27 15:46:29.313] [Pid:(10494)]executeForCursorWindow took 0ms - succeeded, sql="SELECT * FROM emoji_keyboard_panel_items_13"
14: [2018-05-27 15:46:29.312] [Pid:(10494)]prepare took 0ms - succeeded, sql="SELECT * FROM emoji_keyboard_panel_items_13"

If you cleared all the data, meaning you had not added or removed any emoji panels, there should only be 12 keyboard panels. 11 templates + the recent emoji panel.

And yet... here it is loading panel 13.

Also this:

11: [2018-05-27 15:46:33.452] [Pid:(10494)]executeForChangedRowCount took 4ms - succeeded, sql="DELETE FROM emoji_keyboard_panel_items_12"
12: [2018-05-27 15:46:33.451] [Pid:(10494)]prepare took 0ms - succeeded, sql="DELETE FROM emoji_keyboard_panel_items_12"

Ignoring the 13th panel, the 12th panel should be the recents panel. Here it is being cleared. That... would explain why it's empty.

There is some logic in place for clearing the recent's panel when we replace emoji panels between updates, but this most certainly shouldn't happen when opening the keyboard.

I have ... no idea how that might happen, but figuring out what the phantom 13th panel is would seem a good place to start the investigation.

Do you happen to be on a rooted system? A copy of the Exi database ( located at /data/data/com.mayulive.swiftkeyexi/databases/exi_main.db ) would let me identify what the phantom 13th panel is, and hopefully where it came from.