Please attach a full session log file showing the problem (using the latest version of WinSCP).

The first time i logged in using WinSCP 5.13.3 it remembers the last directory browsed from previous version installed. (5.13.2) I got prompted with a dialog box stating that the shell was incompatible and preferred shell is (BASH) (Sorry did not take any screenshot)
The WinSCP application only option from there was to close the SFTP session, so i could not connect at all with winSCP 5.13.3 to a saved server with an old path that was removed.

I had to downgrade to WinSCP-5.13.2, login and then WinSCP could handle that the directory was not present anymore and changed directory to the default for the user: ~/
After that i could upgrade to WinSCP 5.13.3.

I think something in the path was not accepted. As i did not take any screenshot i can not say for sure. I have tried to reproduce the scenario once with the instruction below, but i did not get the exact same behavior.

1. Create a directory in you remote SFTP server.
2. Startup WinSCP and login with SFTP.
3. Change directory to the newly created directory in the remote SFTP server.
4. Close WinSCP. (WinSCp will remeber the last directory)
5. Remove the directory you created in the remote SFTP server.
6. Open WinSCP and you will get an error message stating that the it was not possible to change directory.
Command 'cd "/mnt/project/Test" fialed with return code 1 and error message.
-sh: line 32: cd "/mnt/project/Test: No such file or Directory.

Issue seen with WinSCP-5.13.3 - downgrading to WinSCp-5.13.2 does not give the error message.
BR
Bolleboll