If notes got deleted for some reason while you're beat syncing, you can just import the tablature again and it will line up with the beat map. If you were note syncing instead then you made more work for yourself and are probably going to have to import the tab into a different track, then select all notes starting from where they mysteriously stopped up until the last note (click on the first missing note to select it, then use SHIFT+End to select all remaining notes), copy to the clipboard, seek to where the first missing note goes in PART REAL_GUITAR_22 and then paste the notes and continue working.
If you import the tab again and find that the notes end sooner than expected, send me the GP5 file. Just know that Guitar Pro doesn't always convert to GP5 very accurately so EOF may actually be importing the file as it is defined.