calibre-web and kobo sync - best practice?

Perhaps there are other users who run calibre-web and use the kobo sync feature. I'm interested in how you use it, since I have a problem with my workflow:

I'm rsyncing my calibre data (lots of ebooks) from the desktop pc (where all the changes happen) to the raspberry pi, running calibre-web. This rsync deletes all ebooks on the pi which are not present on the pc.

The idea is, that calibre-web only converts those epubs to kepub, which I do want so sync. On the fly. After a rsync, these kepubs would be deleted, which should not harm since they could easily be re-generated. But what I see is that calibre-web tries to kepubify all (!) epubs in the background. At least when I want to lookup my Kobo Sync Token, calibre-web starts this background-convertion (not sure if it happens on other occasions).

So I would like to know if something's wrong with my workflow. Converting just a few epubs to kepub during the sync process is what I would like to rely on. But this background-convertion takes a lot of time and disk space and is a waste of energy since all kepubs will be deleted by the next rsync.

Is there a solution for this? Or, how do you use/run calibre-web?