I have never seen this behavior with SQLiteSpy, even if I'm doing an update. I happily use SQLiteSpy and RM at the same time on the same database.
The problem I do encounter is that I can't exit RM with a backup if SQLiteSpy has the database open. Something about RM's backup procedure apparently tries to lock the database in a way that conflicts with SQLiteSpy. Exiting RM without a backup is always fine. It's just the backup that's the problem.
Finally, I try to avoid updates, but sometimes they do seem necessary. Usually, my updates "just work" and the newly updated data is immediately available to RM without incident. But in some situations, I have to run the Rebuild Index procedure inside of RM after one of my SQLiteSpy updates. Otherwise, there are indexing errors in the RM user interface. I think Tom understands the reason for this, but I confess I do not. My understanding of relational databases and indexes is that updates to data are also supposed to update the indexes automatically. I seldom encounter this problem, even when making updates, even when doing inserts. So I don't understand why sometimes I do encounter this problem.
I am using SQLite Expert Personal 5.2. It also happens with SQLite Expertt Personal 184.108.40.2066. I I have gotten the database lock message when SQLite is open and I try to open RM7.5 or update something on the edit screen like the residence date. But I get it when RM7.5 is open and I try to query the database also. I don't do it everytime I do those things but it happens occasionally. I am trying to remember exactly what was going on in both programs. I think I may have updated a date in rootsmagic. I usually do not press save. I just press close. And the changes are saved. I do remember being on that screen and then running a query.
I sometimes have problems when I do a compact in RM. It never ends. So I do the 3 finger salute and end RM. I have the best luck re-indexing the file in SQLite. I am not sure what VACUUM does but I use it and then reindex it.
So far the only deletes I do is blank death dates.
I seldom do backups. I prefer making copies of the file before I do the deletes.