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NI's code should be excluded! Many VIs are installed as part of LabVIEW in the C:\Program Files (x86)\National Instruments\LabVIEW folder. These should NEVER be modified outside of installs/upgrades. I started a Mass Compile and, whoa, it did much more than I expected! It changed and saved hundreds of files. I let it run for about a minute, got too nervous, and stopped it. I didn’t think to back that up. Now I fear my LabVIEW installation is dirty. NI SR#7722650 says "It does go outside of the specific folder if the VIs in the specific folder depend on another VI outside of the folder. When it goes outside, it is just opening the VI and resaving it in the current version of LabVIEW. Because your VIs depend on some VIs in the ... vi.lib it went and resaved them. But, they are already in LabVIEW 2015 SP1, so it will not change anything in them. It does this to ensure the VI is looking at the current version of LabVIEW and not an older version." If that is true, why would installation of a version of LabVIEW install VIs of older versions? Make sure all vi.lib VIs are already compiled for that version.
I found https://forums.ni.com/t5/LabVIEW-Idea-Exchange/Force-Recompile-option-in-Mass-Compile/idi-p/2659839 which discusses whether or not LabVIEW Mass Compile changes files that are already up-to-date.
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Declined for reasons listed in post by BoKnows above.