I am a little confused by the trouble that you are having. What do you mean when you say that you "mass compile, the directory changes are not being saved in the individual VIs?" When you "compile and then recompile a folder," what do you mean that "the same directory links are performed again?" By mass compiling, your VIs will be opened and saved in a different version, but paths to your own subVIs will not change. Do you have a VI which you are compiling in multiple versions of LabVIEW? Can you give me a step-by-step for seeing the same problem that you are experiencing?
I have versions 7.0, 7.1, 8.0.1, and 8.2.1 all living happily on my machine and I do not experience strange behavior when I mass compile any of my LabVIEW directories. I am sorry that I have misunderstood your problem. If you can describe the scenario for me, I can suggest how to avoid it. Thanks,
Mike Duffy
National Instruments
Applications Engineer