So, I know you have it clearly marked to not save over your existing save, but I accidentally did...... totally my fault.

I just wanted to check out the mod, so I added it, loaded up my save, to save time, and explored the idea. While I was testing it, I made some progress in the base, and accidentally hit save. THEN I realized my pump jacks were putting out 10% of the oil of previously. Then I noticed all the other patches were at 10% too. By then it was too late.

Now my 200 hour save has changes made that I don't know all of them, and how to reverse them. Removing the mod didn't do so.

I tried the editor, but I don't know how much they were putting out before. I checked out the mod settings as you said the 10% feature could be changed in the settings. no dice. now my only hope is to blueprint my progress and start over. Is there any hope?

You would need to call the manipulate_resource_entities function in scripts/resources.lua but with reversed calculations. Should be possible in the game console. Some resource entities that had <9 left were removed and cannot be restored. There will also be some rounding errors (what previously was 21 is now 3 and will be 30).
The setting only affects not-yet generated resources

Doesn't it make more sense to only affect resources that haven't been generated yet? You can add a setting for it to 0.1x the already generated resources as well. A mod like this should be added at the start of a run, so it doesn't really need to affect already generated resources imo.

What I actually came here for:

I added the mod to one of my saves to test it out, generated an underground level, and then removed the mod again. The world is in editor mode, so I went underground and generated some more chunks. When I zoomed out to the max (before it becomes map view) I noticed small flashing rectangles appearing randomly (they remind me of the rain in Dwarf Fortress Classic).

I uploaded the images to the main Factorio Discord: https://discord.com/channels/139677590393716737/231518135231053825/1456961550450429973
I can also provide the save, but I'm not sure where to upload it.

I'm wondering it this an intended feature meant to show an impending cave collapse, or if my RAM/CPU/GPU is dying (Lenovo Diagnostics didn't find any issues though, and I haven't seen the rectangles in other saves yet).

If you removed the mod, underground surfaces will generate grass floor. A zoom level this high lets you see the boundary between chunks that are not yet generated and already generated ones.

Doesn't it make more sense to only affect resources that haven't been generated yet? You can add a setting for it to 0.1x the already generated resources as well. A mod like this should be added at the start of a run, so it doesn't really need to affect already generated resources imo.

It should be added at the start, but that's not reality for most players and it's mechanic doesnt break existing games, so I explicitly want to support that. Maybe I'll add a command to reset resources, but it is not recommended to remove any mod from a serious game. It is always possible to disable resource generation in the underground.

The brown tiles in the image are also grass, grass 4, and the black tiles are "out of map" which was generated by Subsurface I think (maybe by removing it). Those chunks are fully generated, but in the minimap there are some unrevealed chunks (which might not be generated).

If it's not an animation from your mod, I'll report it to the Factorio devs.

Apologies if I sound rude, I just wanted to be clear.

Turning off the "show decoratives" graphics option fixed the issue for me. I still have no idea how it happened.
I also checked for Windows & Lenovo updates, and updated my CPU (has integrated GPU) manually be getting the update from their website, but the flashing still happened until I turned decoratives off.

I couldn't really figure out what you mean, I only saw small blue rectangles on the pictures, but not flashing.
The mod does not add any animations

The rectangles randomly appear and disappear in different locations, that's why I called them "flashing rectangles", but maybe it's it clearer if I call them "random blinking rectangles".

In-game it looks like there are around 15 of the flashing rectangles at once, but in screenshots only 0-4 show up, probably because they disappear so quickly (but they eye still registers them).