There are various options.

a) You could see whether the EasyPopulate addon will work for your needs. Some folks like it. It doesn't care about the table prefixes.

b) If your "other" store is no longer "live", then you could rename the desired tables before exporting them.

c) You could export them with the prefix name, and then import them to your new server. Then rename them after importing.

This of course assumes you're using the SAME version of Zen Cart on both sites.