Assuming you are referring to this patch, I guess you could try Xkas Anti (backup and there is no guarantee that it would work). Otherwise, you need to port everything over (with the exception of that patch) to a new ROM to get rid of that patch.
Here is the new rom. It has the SMB3 inventory and alot of fixes and of course the levels are now a bit long but are still the same. I switched now to Asar and AddmusicK. So it doesn't crash the rom in other emulators like BSNES for example i just tested that today and it didn't crash anymore.
http://bin.smwcentral.net/u/20391/SMB3ARedux1WorldDemo.ips