I have used UNC paths with desktop a few time. Mainly when i had a dir structure with dependant files etc. Worked fine for me and as you say meant in theory i only had to set one root folder location when porting around.
I'd say it depends on your organisatinal structure.
Some companies change which servers are tied to a mapped drive on an infrequent basis and then rollout the new mapped drives via Active Directory to all staff. In such a case, it would be beneficial to reference the mapped drives as the server names would change.
Otherwise, if a company isn't using fully standard mapped drives or if the servers are generally going to be static for the next few years, it may be safer to use the UNC paths.
Again though, I don't think theres a standard answer for everyone.
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