as the title says, I've found a fix for the disppearing deposits. stellaris already has a system for this, using the functions and . these functions call to at . the fix is simple but tedious to do all at once. you need to make an if statement under the function, saying that if the planet has deposit x, give it the planet flag deposit_x. then under , add an if statement saying that if the planet has the planet_flag deposit_x, add deposit x to the planet then remove the flag. an example is:
for setting the flag under , and
for restoring the deposit and removing the flag under . this works because when the ecumenopolis (or other planet change that wipes deposits) is done the order of events should be, and almost always is: 1. save deposits, 2. clear deposits, 3. restore saved, 4. set needed flags, 5. change planet class.

Here's a pastebin to the fix. The entirety of the file is in there, with the only modifications being the changes for these deposits, so pasting the whole thing over a copy of the file should make it work properly
(side note: I apparently can't comment because I don't own the game myself technically, I'm borrowing it from another account lol)
https://pastebin.com/exFRQpJr