Please provide your server log as well.
If you are able to repeat this test, please this time only, enable debug in the add-on settings > advanced. Provide an updated Kodi log, thank you.
Two changes happened. The server implemented to it's core, tracking of modified items replacing the bulk of the server plugin Kodi companion which now only tracks deleted items.
Second change is for pooling stacked items, the server now provides the key that designates stacked pooled items. I would have to see an example capturing when the issue arises. I will retest this to make sure.
Edit: I've retested movie stacking and it works here. I added an extra version to one of my movies and I still only have one entry. This was done while Kodi was offline. I'll await your other logs. Are you stacking using the web interface or file naming?
I am fairly certain 4.1.3c (you can sideload it as well) will resolve your issue looking at your logs. Keep me posted, thank you!
Edited by Angelblue05, Today, 04:49 PM.