I had something like this happen once. Never figured out what caused it. I used VBA to fix it.
I have tested this. [Apparently not well enough! I had an error in how to iterate through the links. I believe it is now correct.]
HOWEVER, I still need to know how to construct the subfolder name for this to work for you.
An alternative would be to add an extra column to your worksheet and use the HYPERLINK function in that column to build the link from the file name given in your current column A. This adds an extra column and puts the link in a separate column from the file name, but
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