I've been using MPEG streamclip for years and have been editing a project in this codec "Motion JPEG A, Linear PCM". But suddenly streamclip seems to have new options and I cant get my new footage to match the codec on the same timeline.
Is not about MPGStreamclip.
MJPEG is considered a legacy codec.
QT can read it, but depending of your QT version it will be available as an export option (in any QT based app) or not.
Go to QT Preferences and if you find an "Advanced" option, click it and check "Show legacy encoders".
In the last versions of QT Player (7.6.6) there is not option.