I don't use the Linux version but I can imagine that your need to delete files in order to save the game is caused by the same issue that I reported in the topic below. When you have bots that "Repeat forever" an action such as chopping down trees or threshing grain which then creates a super-tall pile of something, every item in that pile is then included in the file being saved, which I have seen becomes a huge file of over 3,400 KB. I suggest that you review this post and take whatever action is similar for Linux so that your game will keep running.
https://itch.io/t/265312/autonauts-take-half-an-hour-to-load