Hi, Jonathan
I don't believe this will cause a technical issue (as the UPN will be different); it could, however, leave to some confusion.
You could move your on-prem user into an OU that isn't getting synced to AAD, then delete the Synced account
It is best practice (if your on-prem accounts are compromised, it doesn't spread straight into Azure, as they are seperate accounts and not tied if anything stop syncing etc) to have Cloud admin accounts as Cloud accounts, so could work well with that.