They're not "corrupted forever". They work fine and have signatures that match them. They can't be restored from the converted nsp to the original xci, but how often do you want to do that? They can't be verified as the unmodified Nintendo files, because they're modified, but if you've converted them with 4nxci yourself then you know they're fine. If you're downloading someone else's conversion then make sure you trust your source.
The reason is preservation, and safety. We do not want to restore them now, but in the future, we will likely want to. XCI’s specifically are not as prolific as NSP and are at greater risk for being lost in the future. If we needed to pull a rare or lost XCI off of a switch, and it was forever corrupted by 4nxci or @duckbill007 , then that would be a truly said thing.
always modify NCA’s in the least way possible, if not at all.