When zero byte files are present, the key (offset) for that file is identical to the file right after. A std::map isn't able to fit key-value pairs with identical keys (offsets), therefore, the solution is to use std::multimap which permits multiple entries with the same key.
This most prominently fixes Pokemon Sword and Shield weather with any RomFS mod applied.
The std::vector instances are already initially allocated with all
entries having these values, there's no need to loop through and fill
them with it again when they aren't modified.
auto x = 0;
auto-deduces x to be an int. This is undesirable when working with
unsigned values. It also causes sign conversion warnings. Instead, we
can make it a proper unsigned value with the correct width that the
following expressions operate on.