@jisip: As above, can you post a screenshot of dir command output and WinSCP side-by-side, showing the differences? Ideally on some small test set of files/folders, not hundreds, if possible.

Some newer files and subdirectories are not viewable in WinSCP when they are in a folder synced to a cloud drive but those files and subdirectories are visible in WinSCP they when are moved to another non-cloud folder. In my local machine folder it's showing 200+ directories, but in WinSCP it's only showing 187.

I am thinking this might have something to do with the permissions the cloud folder is modifying.

Please check and advise.

@RickMarengo: Thanks for your report. I assume you have meant "LHS pane". I have sent you an email with a debug version of WinSCP to the address you have used to register on this forum.

I cannot see an answer in the posts here and believe this is the same problem as I experienced in WinSCP:
I see my remote FTP server on RHS and on LHS I see the pane with my (in this case) c:\Users\MyName\Documents\.
You cannot see any folders underneath the (local) Documents directory in the RHS pane of the WinSCP application BUT you can see them in the local Windows Explorer area. This is pretty frightening as you wonder if you have maybe clicked a Dropbox option to remove your files from you PC and only keep them on the cloud.
I do not know if it is due to a Windows update, a drop box update or a WinSCP update.
I have not found a soluton for this and try the dropbox forum/ support to see if they are aware of this and wether they can do something so it is fixed seamlessly.
I am not aware if similar tools such as SVN, iCloud, etc. have the same problem.

@ravind777: Can you post a screenshots of both WinSCP and File Explorer?

Local directory are not displaying all the folders and files from locally mapped drive. Same can be viewed in Explorer. Notices this issue only in Windows 10. Windows 2016 shows them correctly.

Do you have the problem only with the "dropbox" folder?
Can you see all files, if you go to command prompt (cmd.exe) and type:

Post a screenshot again, please.

Here are the screenshots

Can you post a screenshot of WinSCP panel with files/folders missing and corresponding screenshot from Windows Explorer showing those files/folders?

I have just upgraded to the latest version (5.13.4), and, for the first time since I have been using WinSCP, I had issues with local folders and files missing. This seems to be random, not related to file type or anything I can discern. Some folders missing, some folders present but not all files showing....
Is there a setting that has changed? I have re-installed twice but this keeps happening.
Thanks for any help.