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Glad to hear you're enjoying it! My recommendation is to re-patch a new ROM and transfer the save in. Might fix the encounters. Can explain how to transfer a save if you need, though tbh I would prefer to do that on our Discord to not flood this post with unnecessary responses :P
Tbh I know nothing about RNG manipulation. Only thing that should change it is the optional PRNG fix (disabled by default) so idk how to help with that, sorry!
It depends on the way you're playing the game, if you're using a pc emulator, best to use the File > Export / Import option, on mobile you'll need to make the newly patched ROM's file name match exactly, deleting the old ROM of course
Glad to hear you are enjoying it! This sounds like a patch error, when you patched the Deluxe patch in, did you use a clean ROM (as in, one without ANY additional edits or patches to it, just plain vanilla Emerald)? Patching an edited ROM with the main patches causes unpredictable glitches. Best...