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If you have delete a scene, the first part of the movie will still be in sync. So, just enter in the first line of the subtitles the "original start-time" as the "new start-time" and do this with the last line in the in-sync part too. This ensures that nothing happens with the timing of the first part.

Secondly, in the line immediately following the last line of the first part, enter the "new real start-time". Now try to find a convenient additional cue-point somewhere further in the movie and enter a "new start-time" for that line too.

If you now press the resync buttin, the first part will stay intact but the second part will be reynced.

If you have more deleted scenes, the procedure is exactly the same but then for each part in between the original (and now deleted) scenes. Just enter new start-times at the beginning and end of the remaining parts.