Hi Serial number 01001473 and 01001474I can't comment too specifically on the speaker (being from another manufacturer) but it's feasible for the cone to have been damaged that way in use - you have a powerful amp and vinyl in particular can put out some hefty low frequency information (not always audible) which can really push a smaller speaker driver even at modest volume. I experienced this happening first hand on very early AE1 mkIII's.
It's certainly the case you may not hear any obvious ill effect, there will be air leakage and the break-up/stiffness/dispersion will have altered but if the coil is undamaged it can be surprisingly subtle. If indeed the coil is undamaged it's another sign they may not have been overdriven for warranty.
The dealer should be your first port of call - they know you as a good customer and will be able to talk to their KEF rep. They may want to inspect the speakers and have them in for repair, at worst you may have to pay for a new driver if they determine it as "user error". Often it's at the dealer/manufacturer's discretion when the cause isn't obvious.
If you let me know your AE1 serial numbers I'll tell you the day they were made to clear up any confusion as to their age.