Just like the time for the cells to merge increases with your size, the cells also lose mass at a given rate depending on their size. The only way I have found to circumvent this is to stay divided at super sizes so I'm not losing 1k mass because I can't catch anyone. For those cells not moving, just let them starve until they return to normal sizes.

I think cells losing mass is a new feature, or at least I definitely didn't notice that when I posted my comment a few weeks ago - maybe they took my suggestion :)