I wrote this tool almost six years ago so I'm no longer well versed in its behavior. Some of the code will exit early on certain conditions but others will press on.
A way you can test which options are patching multiple times would be to use a diff tool to compare the old and the new for differences.
This is still not reliable because certain options will react differently depending on the palette of the texture being examined.
There is no good reason to remove the backup/restore functionality as this will ensure that you will always start with a known-good version.
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