It seems as though you have asked this question before and was given the same advice quoted below.
(Once you get your program setup to your liking, you can export the same registry key and store with your backups. That way, all of your preferences will be saved in an easy to reapply method - just merge back into your registry.)http://forum.bolidesoft.com/viewtopic.php?f=2&t=3669
I had the same problem. The operation "update movie details" was always overwriting my movie covers.
Finally I decided to disable the cover import all together.
In registry (regedit) go to HKEY_CURRENT_USER / SOFTWARE / filmoteka
and set value DontImportCover to 1
Hope this helps!