I have a mkv that has literally one frame I want to remove, I tried using DVDVideoSoft's Free Video Editor, it works fine but the problem is it not only deletes the subtitle track, but if I save the subtitle track with aegissub, then cut the video. The subtitles are for whatever reason out of sync by about a second after the edited portion, despite only having removed a single frame.
Are there any video editors out there a bit more friendly toward mkvs?
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Given Free Video Editor apparently did the job when it comes to removing the unwanted frame, try this....
Install MKVToolNix (it includes MKVMergeGUI).
Open the original MKV with MKVMergeGUI. Add edited version (the new MKV). De-select the original video and audio tracks. Re-order the remaining tracks if you so desire. Save the output as a new MKV.
If the subtitles are still out of sync after the point where the frame was removed then logically more than one must have been removed. However....
You could extract the subtitles from the original MKV (gMKVExtractGUI can do it if need be) and adjust the timing. I don't use aegissub but I assume it can. If not, Subtitle Edit will. You'd highlight all the subtitles after the edit point and move them forwards or backwards by the same amount. Save them, add them to the new MKV (de-select the existing subtitles) and save that as a new MKV again. It might take a bit of trial and error to get it right, although Subtitle Edit should let you preview the video with the subtitles while adjusting them.
Oh that's strange, the program won't do it again, I must have made a mistake or it did actually save it editing out a second. I don't suppose there's another editor I could try that can cut out single frames? Or am I screwed because of how the video was encoded (something about keyframes?)
I believe Free Video Editor cuts on key frame which in case your MKV contains h.264 encoded video may be 250 frames (10 sec) apart.
If you really want to cut out just one frame you could either use a "smart" editor like SolveigMM Video Splitter that just re-encode around the cut (not sure about the subtitles) or you could use a NLE editor which means re-encoding the whole file.
You can use Avi-Mux GUI (see here) to cut video & subtitle at the same time (using MKVMergeGUI to make a new MKV) or like said by hello_hello extract the subtitles and cut/sync them in Subtitle Edit
If it's an mp4 file (AVC video and AAC audio) in an MKV container then MkvCutter can be used to remove a single frame without recoding the whole video - but it won't keep the subtitles.
In that case, as mentioned previously, you would put the original and new videos in MkvMerge and select the streams you want to keep.
The cutter makes 'cut lists' which are the frames you want to keep.
If you wanted to remove frame 301 from the file, you select 0 to 300 for the first cut then 302 to end for the next.
The list is then processed and recoding only effects the area where the cut occurs.