Error downloading protected files

We use the s2member-files option to upload the weekly PDF of our online issue. With the most recent update on a partner site I manage, suddenly users are receiving an “Error: Failed to download PDF document” when attempting to open the downloaded PDF (which has me worried, so I have not yet updated s2member on our own site). When I access “Download restrictions,” it says the potential error is with GZIP. After reading the directions, it wants me to add some code to the root .htaccess file. However, if I attempt to modify the .htaccess file in the wordpress root as requested, our FTP uploader states “Critical file transfer error” and will not allow the modification through.

Up until last Tuesday, all files were downloading just fine. Is there anyone that can help me fix this? Until then, our users cannot access any past issues, and our current issues have to be on our public media file (and therefore, searchable by Google and anyone savvy enough to figure out the filename).

Hoping someone here can have an answer. We were dealing with some malware and have had a full clean-up of the site, and now when I access “Download Restrictions” the warning about GZIP issues no longer appears, but all downloadable files via the secure s2Member link are still unreachable.