I've been updating one of my customs, and all has seemed to go well, up until I save, close EoF, and reopen/reload the notes file. All of my changes are undone, the beat offset is back where it was prior to saving, and my effort ends up being for naught. Any explanation/purpose for this?

What version of EOF are you using?  It could be the wrong project file being loaded or it could be an error saving the project (usually you'd get an error and the save cancels and the project is still indicated to be unsaved).  When you close EOF, does it still ask you to save changes?  If you can send me the project (.eof) file, I can test it out.

That's just it. When I close EoF, I get no prompt to save changes, and no errors other than fret hand position errors, which are unnecessary, as the positions have always worked just fine on the current version of the CDLC. However, dragging the first beat measure seems to have done the trick just fine as opposed to using the function.

I can't reproduce that, are you using the 3-11-2017 hotfix?  When I open a project where the first beat isn't at 0 seconds already, I can use "Beat>Push offset back", it works, and when I save the project, reopen EOF and open the project, my changes are still made.

 

If you can reproduce the problem with a specific set of steps that begin with opening EOF and opening the project, please send me the affected project file along with those steps.