Thanks to the forum post from rkfg, I've been forced to investigate the SQLite backend internals. I've discovered a design bug in the way Tagsistant concurrently accesses an SQLite database from different threads which frequently produced a "database locked" error message and prevented normal operations. To fix this, I've introduced a mutex to protect and serialize the SQLite access. This seems to give Tagsistant a lot more reliability, especially when the deduplication thread is triggered.
The release 437 from Subversion trunk implements this change.