Sorry, but I didn't find out how LPX organizes its custom icons. Apparently, ID_0999 is referred to for that purpose, but it's only that big "+"-sign. So far, I was not able to track down the reference to the added custom icons itself... but LPX should keep track of them.
Anyway, it is not possible to organize custom icons by folder or alike. You have to do it "by hand".
Maybe... one day... you never know... 🤓