So you can download the same scan correctly on some (most) sites, but not on this one specific site?

It is really difficult to help you, if we cannot identify where does the corruption happen.

martin wrote:

Make sure you transfer the files in binary mode
https://winscp.net/eng/docs/transfer_mode

I did set the transfer mode to binary. That was the last thing I tried before I posted here. Not easy for me to get original scans from here because they are off-site. During my troubleshooting I did go to the site and watched them write on the form and scan it. The image was perfectly readable and the signature and other hand-written filled portions were perfectly legible and dark. When I came back to the receiving site, the ink sections are either not there or have gaps in the writing. Another odd thing, we have this exact set-up with other clients, but this transmission problem seems to only happen at this one site.

Make sure you transfer the files in binary mode
https://winscp.net/eng/docs/transfer_mode

If that does not help: if you transfer a file back, and open it locally, are the files readable or not? Can you post a copy of a test scan before and after a transfer?

Handwritten portions of scanned documents are showing faded, unreadable, or missing after transfer with WinSCP. I have already tried a different scanner, the documents are clearly dark and legible after scanning when viewed on the PC. After they are transferred, the handwritten parts such as check marks and signatures appear unreadable (either too light, broken up, or not there at all). I have tried slowing down the transfer rate. I have tried setting the transfer to binary. I am at a loss. What could be causing this issue and how can I fix it? Please Help.