Let's try to explain. Us we do some jumps between versions because we know in deep the application and in some case we've added in documentation sobre explanation about large jumps between version. Our suggestion always is upgrade step by step between previous version to next version. Is more tedious but more secure for user. Althought sometimes we've explained this large jumps we do not want to introduce as general documentation because that will cause more confusion than benefits.
About using Hypersonic we encourage switch to MySQL, PostgreSQL etc... for productions environments, Hypersonic is not good option when you're on production, hardware disk failure or bad shutdown can corrupt this database more easily than other ( we got some bad experience on it, and then is very difficult on not possible recover the database ). With OpenKM stopped can log to Hypersonic with some applications like aquafold ( obviously with Mysql or PostgreSQL is more easy doing it because there's a process yet running).
After changing war file, good practice is also remove /webapps/OpenKM and work/Catalina/localhost.
My suggestion for you will be:
1- Install fresh 6.3 with Mysql
2- export all data with export utility and import into new based on MySQL
3- About importing users and folders, some sql queries from here
http://wiki.openkm.com/index.php/Migrat ... .11_to_6.2 can help you
Finally, sorry for our actual documentation status, we're working on doing entire new. We've abandoned the wiki, I do not know if we had not using correctly for our purposes or had been a mistake choosen it, now we got a messi. Meanwhile patience, we got about 4 months of hard working until we get it.