For some reason whenever I upload a VTT file and make some changes and then save the file, Subtitle Edit removes all the Caption Numbers. I know its optional but your backend needs these to properly process the VTT file for some additional features. Is there a setting that I'm missing so that Subtitle Edit preserves the Caption number in the VTT file.
As you can see this is what it does.
[Attachment 48267 - Click to enlarge]
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In the "Save as.." dialog there are two choices for WebVTT. One with and one without cues.
Great that solved it.