I opened the Access and SQLite databases you provided and they both contain 1,258 rows. So all of the rows that are in your Access database have been synchronized in QSO Relay.
I wrote two queries to break down the number of contacts per year for each database, and here are the results for Access and SQLite respectively:
As you can see the number of contacts per year are identical. So I am confident that all of contacts have been sync'ed.
QSO Relay only selects rows from, and inserts rows into, HRD Logbook - it does not delete HRD rows. The Delete Contact feature only deletes rows one at a time from the QSO Relay database.
So I would have to assume you may have accidently deleted all contacts made after the contact with VK3ERW on 2015-05-29 12:25:15.
HRD Logbook creates automatic backups of your database periodically, so you should be able to recover your lost rows if you can locate the archive made immediately before the data loss.