NijiNeko If the original Spine projects have not been lost, a few hundred projects is not that many. Using the export shell script that we made available, you can re-export all Spine projects within a specific folder. Unless re-exporting is truly difficult, I recommend repacking the textures in PMA.
Davide, who is responsible for the spine-pixi runtime, will be away for a while, so he may be able to advise you when he returns, but for now, I think it would be best to look for an easier way to repack the textures.