Framerate change with no cuts

[CBServices]

I have an old .flv video file that I'm trying to swap out the audio track on, and hopefully change the format to something more standard.
When I load the file in Lossless Cut, it shows 30fps for the video track. The same framerate shows in VLC if I play the file.
It's got an H264 video codec, and speex (ugh) for audio.

I tried swapping in a new audio track (aac codec) from another file of the same length, by loading the flv, then dragging the other file in and selecting to add all tracks from the new file. I then deselected the audio from the original file and the video from the new one in the tracks dialog, and exported to an MP4 file. I'm not doing any cuts - just replacing the entire track wholesale. I've done this plenty of times, and it's always worked fine.

The resulting MP4 in this case, though, showed 12.59 fps.

I've tried swapping in a different audio track, with the same result.
Then I tried extracting the individual tracks from the original FLV from the button in the tracks dialog, leaving me with a video only file - still 12.59 fps.

Interestingly, the audio track wasn't extracted as far as I could see.

I tried loading the same flv in MediaInfo from MediaArea.net, and it shows 30fps for the video track, followed by:

(1 Ref frames) (1 conformance errors)

This seems to me like it might be a slightly corrupted file, but I'm not sure.
I've also noticed the video codec is listed as AVC in MediaInfo, whereas Lossless Cut shows it as H264
I can't say that the playback on the original vs the edited 12.5fps version seems any more or less choppy, but I've only sampled a tiny bit of it.

Is it reasonable to think the conformance error is actually something to do with a framerate reporting error? I know nothing about the flv container to know if this is possible or not.
I'm wondering if it's actually a 12.59fps track, but the error is what's causing it to show 30fps, but as I said, I have no idea if this is possible or not.
Or is it something to do with the different codecs reported? Is LC thinking it's a different codec than it is, and this is breaking the framerate?

Any ideas from anyone would be appreciated.

[nwwsw]

You can try and use mkvtoolnix if you just want to replace or extract the audio track.https://codeberg.org/mbunkus/mkvtoolnix