What I'm writing might sound harsher than it's meant, but it's late for me and I had a stressful day. I'm sorry, I don't want to offend anyone. This is just for education purposes.
After looking in the mod and rpa, I can say, it is very unlikely that the mod deletes ANYTHING from the Ren'Py archives. What I can tell you is, that you probably get an error message that an image is missing.
The error message is misleading, since not the image file is missing but Ren'Py's image displayable.
Those definitions look like this (code from game, but changed for reasons):
Python:
image e7_example:
"e7_1" with dissolve
2
"e7_2" with dissolve
2
"e7_3" with dissolve
2
repeat
This is an example of how multiple images are defined as one displayable image, that showns them in a sequence. Those definitions are found in the script.rpy of the game
and the mod. The mod has them for mod purposes (overwriting other stuff), obviously.
Since the mod has the script.rpy of the old game versions, the displayables for the new content are not present. If there is an archive and the same file as non-archive version in the game folder, Ren'Py will pick the unarchived one (the one that is not in the rpa-file). So, Ren'Py takes the mods rpy file, doesn't find the definition of the displayable and says: Meh, can't find the image your are talking about.
I hope my explanation above is helping you to understand, how a mod can provoke such an error, without actually doing what you suggested is happening, especially if it is an outdated version.
If you start the game and it deletes files from the Ren'Py archives, there's something different at work. I don't mean the mod which has python code only to define variables and do some basic Ren'Py stuff like accessing and changing some config.label_overrides, config.character_id_prefixes and config.overlay_screens and stuff (
and no system calls at all).
Cheers!
