If a restart of the SFTP server help, with no change on client side, then it does not seem to be client (WinSCP) issue, but server-side issue. We cannot help you with that.

If you post session logs files (and screenshots) with different results (without and with the subfolder) before and after server restart, we can take a look. But I do not expect this helps anyhow. Make sure you use the same local machine each time (you screenshots seem to be from different machines).

When we restart the SFTP server, the folder are showing like this mentioned on the below screenshot,

Today again the folder were not present on the GUI of WinSCP. Could someone help me to fix this issue

Today again the folder were not present on the GUI of WinSCP. Could someone help me to fix this issue.
Please see the below screenshot.

I did mean "I can't see the subfolder's underneath root directory in WinSCP"

What does it mean "sometime automatically disappear"

We have asynchronous logic app which will be placing the file on regularly basis and it's an automation no manual intervention. So sometime the sub folder is not present that is the issue.

What does it mean "try to login to the SFTP machine the folder and all the details are present there"?

Client is using WinSCP to login and checking the files, and on the backend we have SFTP server the file are sync with Azure blob and we can see the folder and data on sftp server.

Can you answer "Can you see/find them using any other SFTP client?"

Client is only accessing data only via WinSCP.

Did you mean "I CAN see"?
What does it mean "sometime automatically disappear"?
What does it mean "try to login to the SFTP machine the folder and all the details are present there"? Do you mean shell login?
Can you answer "Can you see/find them using any other SFTP client?"?

I can't see only root directory under that we have SFTP folder which sometime automatically disappear on WinSCP, when we try to login to the SFTP machine the folder and all the details are present there. But on WinSCP GUI we can't see it.

Sorry, this is too vague.
Do I understand right that you cannot see/find your files and directories on the remote server?
Can you see/find them using any other SFTP client?

Hi Team,

I am facing one error the root folder and sub-folders are also not showing in it.

What is the issue, we have not made any changes to SFTP server or to the WinSCP software.