Well, it's "safe" to update, if you have the jailbreak bridge installed. The jailbreak will be kept, all other modifications installed on main are wiped -- but you can reinstall them after the upgrade. Of course, there's no guarantee that they continue to work, but most of them will. An exception is everything that is Java-based and non-trivial -- the lab126 guys must have really fallen in love with their obfuscator tool.
And, should everything else fail, you can always downgrade to 5.3.1.