Hey, from my experience you get empty groups in CE when you mess around with the sort ordering of the groups and the “All channels” group specifically. I usually leave the “All channels” group with sort index 0 at the top and then I sort my own groups with sort index 1 and up in tvheadend. You might be able to run other groups/tags with sort index 0 but if “All channels” gets moved as the second group, then the groups get empty.
“If i delete all the recently added m3u linked channels, they reappear again?”
As long as you have Kodi connected to tvheadend it will synchronize. You can disable some things under Settings → PVR & Live TV.
In general I would recommend not to do any changes what so ever in Kodi and all the changes either in TVHeadend or the .m3u file. You should be able to do pretty much everything there.