OK, after a bit of messing about, I figured out a solution. However, not being familiar with Windows, I’m not sure if it’s actually safe, so any further comments would be appreciated.
The reason the file was not showing up in the third-party application file managers is that the Nextcloud folder permissions (Windows “mode”) are set with the -s (system) flag in Windows. You can verify this with the dir command in powershell. This makes the third-party applications ignore the folder.
I have removed the permissions with the following powershell command in the parent folder:
attrib -s .\Nextcloud
Everything seems to work fine now - you just lose the Nextcloud symbol in Windows explorer. Hopefully nothing else breaks I guess? If anyone knows why the system flag is required please let me know.
UPDATE
Actually, in my case, there is a slightly better solution. By setting the read-only flag you maintain the Nextcloud folder icon and the third-party apps can still read the folder:
attrib +r -s .\Nextcloud
Further reading: