When I changed permissions on an NTFS drive, all files are hidden in Finder. How to make them visible again

You might want to try the application A Better Finder Rename. It has a built-in function to convert Mac file & folder names to legal Windows file & folder names:

Naturally, somebody will come along later and throw a smattering of regex in a bash script for you to puzzle out, but ABFR does this kind of thing so easily. It can even create a droplet app onto which you can 'drop' files & folders to be processed. It is a handy tool to have in your toolbox if you aren't a strong programmer, or don't have the time, or both.

This is probably due to how Paragon driver handles native NTFS compression. If I understand their docs correctly, it can un-compress on-the-fly, but cannot actually write the file back in compressed state.

From their faq page:

14. How does the NTFS for Mac® driver handle compressed files?
    NTFS supports its own compression feature. It is impossible (without a special copy routine) to copy compressed files or directories “as is” - because after the reading step we get the uncompressed file or directory. However, if the destination folder is compressed (on an NTFS partition), then the file or folder will be compressed too.

You can confirm your suspicions from Windows, by using standard Windows tools: https://technet.microsoft.com/en-us/library/cc976811.aspx
(Unfortunately, I haven't found any tools that can confirm it from Paragon)