There are two places files could be - in the original Stars hand history folder, or in the PT3 processed folder. After we read in a full file and auto import is stopped the file is moved to the processed folder so that PT3 doesn't need to re-read it every time auto import is started.
To import from the processed folder go to the Manual Import tab, click Import From Directory, and choose the C:\Program Files (x86)\PokerTracker 3\Processed folder and click OK. Expect lots of duplicates (and it's not a problem.
Then after that click File --> Setup Wizard and run through it - that will import all of the files in your hand history folder and move them.
Once that's complete all of the hands you have should be imported.
If you continue to experience these problems,
please follow this tutorial and report the problem with log files so that we can figure out exactly what is causing this behavior and get it fixed.