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It sounds like the files in question may have some limiting attributes. To take a look at the attributes for files in a given file:
if the result is:
Then you have no attributes assigned to this file, and the problem is likely somethng else, if, instead you have one or more letters, such as:
Then you have some form of restrictive attribute, that is likely preventing you from modifying the file as you would like to. To get a discription of the specific attributes that are assigned to a file, I would suggest 'man chattr', which will discribe the attributes and give you the format to modify them with the 'chattr' command, such as to remove the 'append-only' attribute in my previous sample, the command would be: