No, you won’t get an error using them online, cause they weren’t super hacked. Online hack checks aren’t worth anything; don’t use them as a basis.
You likely modified all of them then. My unmodified mons are fine. Also, they likely appeared “legal” (even if they actually weren’t) cause PKHeX previously didn’t check for it. It just means they were illegal to begin with I reckon. If you like, you can upload some of the mons and we’ll look at it.