This happens with battery replacements more often than you'd think. I've had three Roadsters over 16 years and in all this time, it did happen once - it is caused by the PTCM losing 'sync'. If this is your problem, doing a re-sync will restore it.
If the re-sync does not work, you did not do it right OR there is another issue going on. BUT, if you say the top really did stop working as soon as you changed the battery, then I would bet a re-sync is all that is needed.

THis is my version of a re-sync and it works for me and has worked for others. WHile the video talks of how to put the top up and down manually, doing so fullly, as described in the video, with the engine running - IS a re-sync.