The patching tool on SNEStuff is broken. It could damage the rom. Make sure to have a backup. I didn't notice any problems with other tools in that utilty.
The problem appears to be that it patches an unheadered rom as though it has a header.
February 26, 2012, 08:57:49 pm - (Auto Merged - Double Posts are not allowed before 7 days.)
The tool uses a special formatting method which adds an extra byte at the end of the patch file. There is a 01 byte placed at the end of the file which signifies to subtract $200 from every address in the patch. This 01 byte is automatically set by the default setting if you have the tool format the patch.this is the default setting. clicking format and continue will cause the tool to subtract 200 from every address in the patch.this setting will cause a 02 byte to be placed at the end of the patch file. this will cause the patching tool to not add or subtract anything from the patch addresses. it is not selected by default.
The problem is if your patch was made from a non headered rom with a different tool then using the format setting from this tool will adjust all the addresses in the patch because you naturally would leave the "intended for headered roms choice" unselected.
Selecting to "continue unformatted" will avoid this trouble but selecting the choice to "never format patches" has no effect because the next time you open it "never format" is deselected.
This all should be explained at least in the documentation to save some headaches.