This sounds like a problem on the Windows side of things, not Linux. I suggest you delete this question and ask instead on Super User.

Linux created the files. Linux can read Windows file systems, but Windows is very limited in reading Linux file systems. So I believe this must be fixed from the Linux side.

As you said, Windows is limited in reading Linux file systems, but exFAT isn't a Linux file system, which is another reason why I think this is an issue on the Windows side. Even if it can be fixed on Linux, which I doubt, you still need someone who knows Windows and knows what fix would be needed. After all, it works on Linux, your issue is with making it work on Windows. This is why Super User which supports both Windows and Linux questions would be a better place.

There's a reason Linux is used for file recovery on Windows systems. If I don't get an answer here today I'll delete this and post it to Superuser tomorrow.

Yes, the reason is that Linux is very good at reading other filesystems. But you're trying to do it the other way around :). But sure, wait if you like, but this already has 2 out of the 5 close votes needed to close it.

Windows knows exFat, so how is it the other way around?

Microsoft created exFat in 2006, so this doesn't seem correct - "Yes, the reason is that Linux is very good at reading other filesystems. But you're trying to do it the other way around :)" --- Linux is keeping Windows from seeing a file written on its own file system.

@JasonF4 No OS has ownership properties for ExFAT. The file system doesn't support ACL's. It's probably some inconsistency in how Linux writes metadata to the exfat FS, but it's rather hard to guess how...

Windows can see the exfat partition on my external linux SSD drive, and even automatically assigns it a drive letter. (I just don't have enough room to move the files there.) Same Linux. Same Windows. Same computer.

exFat issues need to be fixed on windows. Linux has support for reading and writing windows filesystem but never ever did anyone claim it is 100% accurate. Repairing a windows filesystem from another OS seems weird to me. Windows has far better tools to fix their own filesystem. My idea would be where I read this "Linux sees the files on that exFat partition.": make a backup and replace the disk?

"I'm considering just reformatting that exfat partition to NTFS," you do know you never ever do something to a partition if you want to restore the previous state? Reformatting means the layer that was there before is gone forever.

Correct. Windows can't read that exFat partition, and those are Windows files. So I'm considering running PhotoRec again for 5 hours, and re-creating those file in a format that Windows will read, since it won't read exfat, Microsoft's own file system. The disk I'm running PhotoRec on is a copy of a failing hard disk, made with GNU ddrescue, and I don't believe it will have any problems, as it's a brand new drive.

(1) You say, “I copied a text file, not created by root or PhotoRec, to the exfat partition. Windows still doesn't see any files there.”  This says that the problem has nothing to do with PhotoRec, and so about 50% of your question is irrelevant.  (2) FYI, permissions problems cause permissions errors; they do not cause files to be invisible.  (3) I hate to insult your intelligence, but are you sure that you’re looking at the same partition in Linux and in Windows?  How?  Can you show us what you’re doing, in more detail, that makes you believe this?

(4) You said, “Back in the late 90's SU was the place to post things.”  Actually, no; Super User didn’t exist in the late 90s.

Did you already check and repair the file system using the MS Windows tools? This is very likely a partition that is not anymore consistent for a long time. Then, corruption builds up to the point that one of the OS'es does not see the files anymore. If your backup is not up to date, backup all you can on Linux, then reformat the drive. Have it checked regularly under Windows if you use exfat or ntfs. Otherwise, you can use linux to check.

@G-Man - This partition was created to do this restoration. I cut it out of my 1TB main partition for MS Windows. So it has not been used for "a long time." It was used once.

@G-Man Re "I hate to insult your intelligence." I get it. It is very odd that Windows says the drive is empty. I simply don't have another 700GB partition around (not even close) to have all those restored files. I got a reply form the forum at CGSecurity (the publisher of PhotoRec) on how to check the partition from Windows with chkdsk. I did not want to touch that partition from Windows, as Windows thinks it's empty. I assume the Site Admin at CGSecurity knows what he's doing. I will be commenting here again shortly.

Silly question - but what exfat driver are you using? It dosen't work out of the box. Can linux see files you add in from windows?

@JourneymanGeek - exfat-fuse / exfat-utils 1.2.8-1 (The latest version that will install after running sudo apt-get update.) ----- I significantly updated the post, with images from Linux and WIndows showing the problem.

@G-Man - I significanlty updated the post, showing (images) that Linux showed 400GB of files, while Windows showed none, and other information.

@Rinzwind - Running chkdsk on Windows, without doing a repair, resulted in the 400GB of files becoming invisible (apparently deleted) from Linux. I added images showing GParted showed 400GB of files, while Windows showed the partition was empty, and of specific steps I took. I will never again use exfat to share a partition between Linux and WIndows. I will be using NTFS to redo this.