I tried different things to avoid the tedium of adding each time the link to the mask file in each clip.
In my case, the mask file is the same PNG file, so I created a track and placed the clips with that filter on it. In theory, I would only have to do the operation of reassigning the mask file once.
The mask filter could be applied to the track and not on the clip.
However, because of the filter settings and also because of the length of the project (less than 15 minutes), it was faster for me to manually relink on each clip.
I was then tempted to export part of the project in lossless UtVideo format, then incorporate that clip into an earlier version of Shotcut and continue editing.
I’m not sure, but you can try to save a copy of that project (once the masks have been corrected). Then you can try to open that project with the previous stable version. The Time Remap filter is not compatible with this regression, but if you did not use this filter, maybe your project will work without problems.
Just be sure to work on the copy of the project, to avoid damaging your original project.