I only change to boot from Luma directly, yes I didn't remove the rxtoolsSo that your Emunand has the sysnand firm. You have rxtools still? It should be Luma handling this, and the ips files should work.
but normally, is that all we have to do with the ips files is to put them in : SD/luma/titles/0004000000164800/code.ips
then go to the config menu and x "Enable game patching" and "Use SysNAND FIRM if booting with R"
after that, boot the 3ds with holding the R button and go into the pokemon game with the ips file working immediately?