Trying to understand timing corrections from HT for SAB

Our team used HearThis for recording Mark. But then after recording they had suggestions for revisions (since the book had been completed 10 years ago). These revisions were made, and included some punctuation changes, which caused problems in the timings. Based on other posts here (such as “HearThis to SAB sound file misalignment”), I was able to use the “Shift Clips” feature, thankfully, to fix the major problems.
But there are still some problems, and I am trying to understand the underlying issues, in order to make the corrections in the right place, so that any future changes in HearThis would not require all of the same corrections. What confuses me is that in HT, everything sounds correct, all recordings are matched with the yellow text lines accurately. But then when using “Export Sound Files” (and choosing SAB, and Audacity, with phrase-level labels selected), it appears that the timing files were not updated to match. Also the *.info text file in the Program Data folder has some problems in the verses that were changed (e.g.the text and line numbers don’t match what shows in HT).
I have then tried to use the “Fine Tune Timings” feature in SAB, but I don’t understand how that works, i.e. which files is it correcting, how those fine tunings are saved, and will those adjustments be saved in case future corrections are made in HT, or will all of those fine tunings have to be done again? And some are not “fine”, since there are still some places where a whole segment/clause is not highlighted in the SAB app.
So I’m wanting to understand the “best practices” in making corrections in the right place after rerecording segments. (It is possible that I messed things up when using “Shift Clips” and renaming a few *.wav files, and now I don’t know how to correct those in the place where it will count.)

Thanks for posting your question. I’m glad you are finding these tool useful and that you were able to use the shift clips feature (somewhat at least) successfully.
Some types of changes to the text (e.g., actual wording changes) will obviously require re-recording clips. Where the changes are merely to the spelling of words, but the recorded words are pronounced correctly, no change is required. (We have a new feature mostly complete, but stuck in a bit of a log jam, that will help you find and deal with those kinds of changes so that the .info files match.) Punctuation changes tend to be the trickiest because as you noted, the recording—at least the combined one for the chapter—can sound fine, but things do not always align. If each clips seems to align to the highlighted text in HearThis, then no shifting or re-recording is necessary. In those cases, the .info file should have the correct information except in places where you manually renamed .wav files. If it does not, please submit a bug report to hearthis_issues@sil.org with details.
Even when everything is perfect in HearThis, there is still the possibility of the highlighting being off in SAB. One cause of this that is easy to fix is if the phrase breaking settings in SAB are not set to match the phrase breaking settings in HearThis. When you export to SAB in HearThis, I think the output window shows a reminder indicating what phrase breaking characters to use in SAB. So that is the first thing to verify.
Even with that correct, there are still some subtle differences between HearThis and SAB that require HearThis to guess a little bit at the timings. Most of time, these result in relatively small misalignments, but sometimes they can be noticeable. Unfortunately, if you use “Fine Tune Timings” in SAB, there is no way for the adjusted timings to find their way back into HearThis, so if you later make additional changes in HearThis, you’ll have to start over in SAB. (I’m not sure how easy this would be to do in SAB but you can maybe just reimport only the changed chapters, if you know which ones they are, so you would only have to redo those chapters.) I am not aware of any reason why entire segments should be getting skipped in SAB if everything is aligned correctly in HearThis, so if that is happening, again please report it as a bug and we will request the necessary information to follow up.
A final option for getting things to align in SAB is to use Aeneas. In my experience, it is not quite as good as the alignments produced by HearThis when everything is working correctly, but for most languages it is amazingly accurate, so it might be an adequate solution. If you try it and are dissatisfied, you can always pull the HearThis timing files back in and go back to figuring out the problems.
If you need additional help, please reply and we will try to find a time where we can work together to sort things out.