Hi!
These kind of problems have been discussed in forum before. Maybe you can find them with suitable search words using Google.

I do not use online logs but I think you should export your unlogged qsos as adif and do manual update to online log with web browser and your adif file.
After that select Qso list/online logs/Hrdlog.net/Mark all qso as uploaded

After doing these two operations you hrdlog should be in sync again.