I re-authored a DVD with DVD Shrink to get a small clip (all audio and subtitles included, in a new DVD folder).
In the original movie, the subtitle appears at 04:11 (four minutes and eleven seconds into the video).
In the new clip, the subtitle should appear around 00:05 (five seconds into the video).

Loaded the .ifo in AGK and elect external subtitles.
AGK processes the files, but the idx file still indicates the original time 04:13 instead of the new time - so although the subtitles are selectable with VLC, they never show.
I can approximate with SubResync and adjust, but it isn't accurate enough, they drift out of sync.

As a side note, the output files from DVD Shrink (not the AVI from AGK), when authored to disk, and played back on the standalone DVD player, manage to show the subtitles at the correct time??