That's right, you have to replace any files that were patched (not only the eboot) by their original counterparts from the original disk.
As you said, some games will work and some others won't. Games that weren't patched to run on 3.55 (games that require FW 3.55-) would work but games that were patched wouldn't work with the 3.55 patches, you have to unpatch them.
CECHL 500GB: OFW 2.50 > OFW 2.76 > OFW 3.41 w/ dongle > OFW 3.55 > 3.55 kmeaw > Rebug 4.30.1 > Rebug 4.30.2
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Off to my summer vacation, might be AFK for a while... Happy Summer!