It's a very very hard migration
http://wiki.openkm.com/index.php/Migration_Guide and during the process should be lost some minimal information like bookmarks, obviously documents, folders and secutiry is preservate, but will be needed migration of users.
Here's the migration guide
http://wiki.openkm.com/index.php/Migration_Guide
From version 4.0 are several upgrades with some difficults
- 4.0 to 4.1 seems easy
- 4.1 to 5.0 is hard
- 5.0 to 5.0.4 seems easy
- 5.0.4 to 5.1.8 seems with medium difficult
- 5.1.8 to 5.1.11 is easy
- 5.1.11 to 6.x has medium difficult
Depding your repository size etc... it's needed more or less time ( always considering your repository is right ). In a good scenario should be needed 2 complete days for doing it, probably more ( I'm talking about OpenKM Team technicals ). The problem you got is that now is necessary doing the work that has not been done in last tree years.
Anyway I suggest you backup your system, reply in other and if you decide to migrate try there.