#991 was not prompted by this.

I just tested this again. I did "Select a theme" / "Install updates for the theme" a few times, and was prompted each time if I wanted to override. Each time I chose to keep the file, and the file was indeed kept. One time (coincidentally right after I had tried recompiling from the shell) I was not prompted for overwriting after clicking "Install updates for the theme", and noticed that the file had been reset, even though I'm pretty sure I didn't do anything that should've reset it.

I tried the process again, and this didn't happen. I even tried running recompile from the shell multiple times, since I thought that might be the problem, but it didn't occur. The logo was overwritten when I switched from one theme to another and then back, but I'm not going to worry about that "bug" right now.

I don't know if there's a bug here, or if I just misclicked something twice. I don't see anything wrong, so I think I'm just going to merge in main an then merge after tests pass.