MUX H264 Streams Transcode MPEG2 streams?

What I would like to do is Remux my H.264 recordings to MKV … and Transcode my MPEG2 recordings to H.264 MKV. Is there a way for mcebuddy to read the file and do what I want… My EMBY recordings are mixed H264 and Mpeg2.

Completely possible.
You will need at least 2 conversion tasks. You can use the Codec selection filter to choose which ones get processed by which profile.
For your Remux task choose a remux profile with a selection filter of only Mpeg4 selected and for your Transcode task choose a conversion profile with a selection filter of only Mpeg2 selected.

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