From the results of beta testing, beta 4 is pretty solid. Although I've changed some stuff for the final 2.6, there will be no file format changes, or anything like that. Thus, anything you do with beta 4 should work in the final 2.6. If you're planning to use 2.6, I would just start using beta 4 now. When the final is [finally] released, just upgrade to it and you shouldn't lose anything.
And just to be clear: upgrading the software does not delete anything. It *will* overwrite files that are included with the software. So, in addition to the application itself, files like the default layout (Default.tlo), and the various sample templates, like the SampleRounds.trt, will be overwritten. Anything you create yourself will not be touched. This is true even if you uninstall the software. It won't delete any files that were not originally *installed* with the software.