Anecdotal time that the AE prefix started on the serial numbers.
1994
Earliest time for AE/EA prefix change. All before this are AE.
1995
Latest time for AE/EA prefix change. All after this are EA.
2004
Mag release changed to wider model.
Source material for the above table
According to czfirearms.us's user jwc007, EAA Witness serial numbers changed from an AE prefix to an EA prefix during their '94/'95 production run.
According to a thread on czfirearms.us, the AE prefix frames can't accept the various caliber conversion kits available for the EAA Witness.
According to http://www.henningshootsguns.com/tech/tech.tanfoglio.magrelease.html, you can tell whether you have a new or old mag release by seeing whether the magazine has enough play to move up and down. The old mag release grips into the notch on the mag with a much smaller protrusion than the new, wider one.