Here’s something you can try. I would try photoshopping two versions of the pickle jar one for the start and one for the end. Then bring them into AE and have the clean version of the first photo fade out into the clean version of the ending photo. Have the original timelapse video as the top layer of that comp, and try using the luma key effect to key out the brightest spots (which would be the yeast).
That’s the easiest way i can think to try removing those. Otherwise i think youll have to piece together patches of clean pickles to cover up the yeast.