Not normally if you make a direct copy, but file sizes can change when you transfer via FTP in ASCII mode.
You may need to diagnose what's actually happening to the files at your end to work out why the sizes are changing, since we can only really make guesses from here.
See if the file sizes change back, and if the files are byte-for-byte identical, if you re-download them and compare them to the originals.
Check what happens with another FTP client.
Double-check that you're using binary mode in Opus, and that the change you have made is actually affecting your synchronize operation. (After making the change, fully exit Opus (via File / Exit Directory Opus) and restart it, to ensure no cached connections are being used. And make sure you connect to the FTP site using the FTP Address Book in Opus, not a saved layout which may store old settings. Verify that binary mode is being used for the transfers by checking the FTP log in Opus.)
Make sure nothing on the Windows side is modifying the files (e.g. to change metadata, or latent changes made just by opening the files in some software, which MS Office can do sometimes).