So after some digging I could solve the problem. Maybe someone else encounters the same issue and this helps:
In my collection of markdown notes was one note (created by the conversion from Evernote) that contained a lot of inline data. The note itself looked fine in the desktop version of Joplin but contained 2 MB of data. This caused the Android app to synchronize up to that note and then stop the synchronization process.
With the very large note removed it all runs fine again.
