Don't worry about the version problem. Let it rebuild.

You will NOT be able to merge the two databases.  It will be difficult to move them to the older server if the newer server handles new messages.

The embedded database is only used to display messages without search. A corrupted database does not affect email flow. In the worst case scenario message won't show when trying to view them without searching, which will get fixed eventually since Xeams only displays messages for last X number of days.

There are two ways Xeams display messages through Message Repository:

• The embedded database - this is used when you try to show "View All Good/Possible/Junk". New entries will be inserted into the database as they newer emails come in. Records older than ten days (or whatever the retention period is) will get removed from the DB. 
• Search Indexes - these are used when a user explicitly searches for older messages. Database is not used in this case

Therefore, even if you can't get the DB migrated or recreated, the problem will go away in a few days, and it won't affect email flow.