If the video framerate is wrong you have a few options:
1. Remux the video to a new container, setting the correct framerate there.
2. Create a "dummy" VFR override file that just sets the framerate, and use that.
3. Create an AVS script that loads the video and does an AssumeFPS on it, and load the video with that AVS in Aegisub.
While option 3 is perhaps the easiest and fastest, it also has the problem that you can't load keyframe information directly from the video file. Option 2 is probably the most flexible one, and option 1 is the surefire way, although it takes some processing time and extra disk space.
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