When you do a manual import you need to make sure that the cache is updated in order to avoid HUD problems. The best thing is to enable the housekeeping options on the Manual Import tab, but if the cache shows anything other than 100% in the status bar at the bottom of PT3 you can update it manually using Database > Housekeeping.
If your computer crashes or you force-stop PT3 then the HH files will not be moved, but in this case there won't be many files so the easiest thing to do is to run Auto Import again with no other tables open and let it catch up before you start playing again.