I don't know if this relevant for PXI, but FieldPoints have a time server setting in max. If this isn't available, I'm sure there are examples available for how to sync time with a server. I remember a specific example for FieldPoint which uses an NI DLL (I think is was called settime.dll) and which allows you to set the time on the RT target. Even if not, I assume writing some code for this will be fairly simple, unless you want a high level of precision. My first suggestion would be to check MAX and look for examples on this site.
I haven't heard of RT commandline commands, but it would be interesting to find out if there are some...
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