Same here, I just ignored it and I don't think there can be any issue with doing that. Why would you serve a notice to quit when the tenant leaves of their own accord? But the RTB site does seem to assume that tenants stay forever until the landlord evicts them!
A problem I ran in to is this - I had a new tenancy just after annual registration comes in, so I registered the tenancy and paid the €40 fee. Six months later the tenant left and I re-let but it was really unclear how to register the new tenancy and avoid a further €40 annual registration charge. I have a couple of apartments with short term tenants (hospital staff) and the first time it happened, I paid the second €40, was promised a refund by the RTB, but unsurprisingly never got it. The second time I added my new tenant to the existing registration and, after many emails, got the RTB staff to remove the original tenant. Did anyone come across this and is there a simple solution to it?