Steps to Reproduce:
A) 1. Add a resource & Select 'Link to a file/website'
    2. Upload a file & choose it
    3. Save
B) 1. Update the Resource
    2. Choose another file
    3. Save
C) 1. Edit & Save the external file (e.g. Word/Excel File) you uploaded originally
    2. Update the Resource from A & B
    3. Upload and Choose the edited file (C.1.)
    4. Save
    5. View the resource. It is still the same original file you uploaded in A)2!

Expected Behaviour:
I would think if you deleted a file that if you made an offline edit and reuploaded it that Moodle would treat it as a new file. Miraculously it revives the old file and disregards the new file.

Workaround:
When editing the file, rename it and follow steps C)2 to C)5. Only now has your editing taken affect and the invisible 'deleted' file finally 'gone'.

MIght this bug be similar to MDL-7660?

Apologies if this is a clone of MDL-2661(very old) but it seems the issue was more about the warning message rather than fixing this bug. I also couldn't find it as a fixed bug for 1.9.4