The mysterious shop books do not apply to your character but still eat your gold. It will show when checking diaries but once you leave the shop, the gold is spent but the values are reverted to what you had before.
I've also noticed that going into the tools & diaries screen sometimes messes up with whatever choices you have made on the current story screen. Possibly certain variables are not global or something like that and get re-instanced when changing between those screens.