I changed times on three AA flights as part of a DONE4 a couple of weeks ago - literally just shifting flights back a few hours.

Also got the 'reissue' comment - queried it and told a new policy.
No charge for the reissue.

I assume they are really looking to only recover any extra taxes/ fines if these have changed mean time, or maybe to have an extra check against not re-introducing a stopover when it needs to be a transit.