YouTrack database started to grow (very) rapidly

Hello, Support Team.

YouTrack version is Build 2021.2.19255, selft hosted. Yes, I know it pretty old, I wanted to update, but when we figure the problem out.

We encountered a very strange and unpleasant problem: we use the YouTrack with the file database (Xodus). 
Our usage style is very moderate (4 users, 50-100 tickets per month).
In the end of May we decided to start to use the Time Tracking feature. There were a problem in our software - it sends a lot of time update API requests to the YouTrack. We found it, rolled back the database and disabled the Time Tracking feature for all projects.
But now our .xd files grow in 1 day like in 1 month before the problem.
The issue is NOT with the blobs/ folder: it feels that ALL data is stored into .xd files, blob is not growing at all.
We have 8Mb .xd files. 
10 files for the historical 3000 tickets (Mar 2023 - May 25).
and 2(!) for just one day.
If I change any ticket property then the .xd file grows to 10-30kB (depends on property).
When I create a new ticket without any attachments I see +200kB .xd file growing.
That's incredible.
Please advice us what can we do to:
1. Clean up the database.
2. Debug why it happens.
3. Restore it to the original state.

Thanks in advice.