For the same Version number SQLA does not support the parallel installation of different builds. You could have an 16.0 and a 12.0.1 server on the same machine, but not a 12.0.1.3537 and a 12.0.1.3598.
Anyway both products should be able to work with a current EBF, be aware that a current EBF might need an upgrade of the DB file before the DB can be run in the current server.
You will get answers much faster on the SQL Anywhere Question and Answer forum http://sqlanywhere-forum.sybase.com/