playing pre-patched CDR backups with Messiah

[swspjcd]

I have several backups of PS2 games that were PPF patched and then burned. The original RAR files were deleted. A good deal of them don't work with the messiah chip. Some boot, but go then keep looping back to the beginning of the game and others just stay at the memory card/PS2 Game Icon select screen. Is there any way to get these to boot without having the original RAR files? Is there any way to BIN/CUE them and then unpatch them?
Thanks Much.