Updates made by reindexing are lost after repository restart

After reindexing a repository with the API in org.modeshape.jcr.api.Workspace, updates to indexes are lost during the next restart of the repository. This has the effect that queries to nodes under FileSystemConnector stop returning results, the index is still used but it appears not to contain any data.

Additionally the file size on local-indexes.db.t keeps increasing rapidly with each subsequent reindex (this is reset during restart).

This is what happens to Local Index Provider's index files (it seems like there is some issue with committing the changes to MapDB):

1) A fresh repository is started and some nodes are created under FileSystemConnector with the JCR API:
local-indexes.db 34168 B
local-indexes.db.p 2066288 B
local-indexes.db.t 16 B

2) After deleting the index files and restarting the repository
local-indexes.db 32968 B
local-indexes.db.p 184 B
local-indexes.db.t 54545 B

3) After reindexing the repository manually:
local-indexes.db 32968 B
local-indexes.db.p 184 B
local-indexes.db.t 2758843 B

4) After restarting the repository index files revert back to state 2), before indexing