One can always move the MySQL form and data files between
different versions on the same architecture as long as one has the same
base version of MySQL. The current base version is of course
3. If one changes the character set (sort order) by recompiling
MySQL one has to do a isamchk -r -q on all tables.
If you are paranoid and/or afraid of new versions you can always rename your old mysqld to something like mysqld-'old-version-number'. If your new mysqld then does something unexpected you can simple shut it down and restart with your old mysqld!
When you do a upgrade you should of course also take a backup of your old databases. Sometimes its good to be a little paranoid!
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