I have exactly same problem, sometimes I need to reformat external unit to use again "disk1"
I can copy and remove file inside, but for usermanager the database is like readonly.
I suggest you what is worked for me for months:
0) Reall all first, and try to understand all first...
1) Backup EVERYTHING: export file .rsc / make backup / export user manager database. /export certificates / export files inside files / etc.
2) copy on one directory the actual user-manager files sqldb and logsqldb (not the backups) NO any "JOURNAL" FILES!!!(***)
3) put sqlite3 from https://www.sqlite.org/2021/sqlite-tool ... 350500.zip
on same directory and on windows prompt go on same directory do this commands:
sqlite3 logsqldb VACUUM
sqlite3 sqldb VACUUM
4) Netinstall the device (I suggest use 6.48.2 netinstall) with the version routeros 6.47.9 + user-manager without keep any previous config
5) Update routerboot to 6.47.9, disable unneded system packages but keep absolutly dhcp and security active (it's not the time to explain), and reboot
6) Reimport CERTIFICATES first, if any.
7) Reimport any file needed
8) import on disk1 or directly on root the user-manager directory with the files "vacuumed", replace existing files if needed
9) reimport .rsc with notepad (or similar) on terminal section-by-section and read first what you set. SKIP USER-MANAGER PARTS
10) When done set user-manager database path accordingly with new directory _TWICE_
do that command on winbox console (copy and paste):
/tool user data
.. sess rem [find]
***: In other cases do not delete for any reason the journal files if exist on a running user-manager
I'm Italian, not English. Sorry for my imperfect grammar.