Windows considers the Program Files folders as "protected" territory, so you might see splash screens and other graphic files take, but anything "cfg" is taken as a "system" file, and does get "rolled-back" to the previous "authorized" version (too many quote marks...
). The Windows behavior varies with other files, so you might well be seeing the Stock game's messages.txt file, which sometimes looks like someone got tired of filling it out about February 1942
- some months there are no reports. Back out all of your mods, make yourself a new folder somewhere, such as "C:\Games", and then <Ctrl><C> the game folder ("Silent Hunter Wolves of the Pacific" or whatever) and <Ctrl><V> inside the new folder to copy what you have over. If you want a short-cut on the desktop, you'll have to make a new one of those. After the move, re-apply all of the mods, and either use MultiSH4 to create a new Save folder (such as RSD or whatever), or empty the existing Save folder. You will have to re-set your screen resolution and all of the gameplay settings, but you won't have Windows trying to protect you from yourself anymore either...
Edit: Oh! as for the traffic, you'll have to find the "shipping lanes", and lurker does have a map - either on the Captain's bed, or somewhere on the sub - that shows where the traffic generally is. You will notice also though, that the levels (frequency) is quite a bit lower, like maybe one fourth of what there was in the stock game because of the "historical" layers that lurker made. You might go an entire patrol with only seeing airplanes, if you don't know where to look. On a side note to that, once an airplane "sees" your submarine, others are directed to "search" in your general area, so you will see even more airplanes than normal. If they see you, change speed (faster or slower, doesn't matter) and change course. Just be mindful of fuel usage and what's in your bunker...