JakubMisek Hi Jakub, thanks for your reply.
After rolling back to the older version, I was able to publish and a much more realistic 180 changed files were published, rather than the 1100+ files that were listed in the Remote Explorer in the newer version.
I was able to Validate Connection successfully in the profile that was giving the Permission Denied error in the newer version. It is SFTP and is the same profile that is working in the older version, erroring in the new version.
What I was able to pin down by looking through the Publish log entries after rolling back to the old version is that when it came across a problem, it just noted it in the log and moved on. Remote Explorer seems to stop. There are apparently some files that actually do have permission problems, not being allowed to be overwritten.