Best way to fix "Interrupted" recordings with wonky Comskip results

I recently recorded a marathon of "The Closer" on HLN. The Comskip processing was 100% accurate on all episodes except for those with the "Interrupted" tag.

On the majority of episodes, commercial processing results look like this:

Straightforward, and accurate.

On the several interrupted recordings, some of the commercials are buried in blocks:

I haven't seen this before, so I tried reprocessing for commercials but that yielded no changes. Might "Fix Video Timestamps" or "Regenerate Video Index" potentially be of value here?

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I wouldn't use Fix Video Timestamps.
Just remux the recording with ffmpeg and then redetect commercials.
ffmpeg -i recording.mpg -map 0 -acodec copy -vcodec copy -scodec copy -dcodec copy recording.ts
mv recording.ts recording.mpg
Redetect Commercials

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Here's the windows cmd script I use to remux. I just drop the recorded file on it, it remuxes and will move the remuxed file to the directory you dropped it from and also logs the ffmpeg std and err out to a log file.

ffmpeg_remux.cmd
@ECHO OFF
ECHO ...
IF %1.==. GOTO USAGE
REM Change current working directory to where this command script resides
%~d0
CD %~p0
REM Use ffmpeg.exe to remux the recording to a new .ts file in the current directory
REM and redirect standard and error output to originalfilename_remux_log.txt
ECHO Remuxing %1
ffmpeg -i %1 -map 0 -acodec copy -vcodec copy -scodec copy -dcodec copy -copy_unknown "%~dp0%~n1.ts" > "%~n1_remux_log.txt" 2>&1
REM Move the remuxed file.ts so as not to overwrite the original
ECHO Remuxed %1
ECHO to file "%~dp0%~n1.ts"
ECHO Press Ctrl-C to keep remuxed file here, or to move it to original directory
PAUSE
MOVE /Y "%~dp0%~n1.ts" "%~dp1"
GOTO FINISHED

:USAGE
REM Need the fully qualified filename to remux
ECHO Drop a file to be remuxed on this command file

:FINISHED
PAUSE
EXIT

It's possible "Fix Video Timestamps" could help here, though I would be surprised if it did.

The issue could be that some of the important indicators (black frames) that transition from a show to commercial were in the part of the stream that was lost during the interrupted recording. If that were the case, fixing the timestamps or remuxing wouldn't have any impact here.

The difference is that your first screenshot is not using comskip, it must be smart detected commercials. The interruptions break the smart detection feature so it has to run comskip, which doesn't do well in this case.

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