The following suggestion would no doubt prove tedious - depending on how many files we are talking about.
Create yet another 'sub directory' perhaps entitled 'Mk 2 Main Directory'. Move all the items to it. See if they can then be deleted in the normal way. If they can you have at least proved that the problem isn't related to the files themselves.
Finally - move each file back again - into the Main Directory proper and delete the sub-directory you created. The other solution of course is 'live with the irritation'.
Their lack of answering your e-mails seems like simple rudeness and a bit symptomatic of an organisation in a mess and typical of the age we live in.

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