I've changed the specific registry entries and now I got back the expected function. There were only five entries to change with a different ssh port.
Thank you for your help.

OK, so it's location profile, not a bookmark.

The profile has two entries, in the Local and the Remote subkeys of the Bookmarks key. And optionally also in the Options and the ShortCuts. You have to rename all of them the same way.

martin wrote:

Please attach a screenshot of a selected bookmark.

See attached hardcopy. First I open the bookmark windows. Doubleclick on any bookmark will not change the directory as in older WinSCP versions.
Doubleclick works for newly created bookmarks, but not for stored bookmarks from older versions.

Please attach a screenshot of a selected bookmark.

martin wrote:

You would have to go to registry and add the port number to the respective key. I.e. rename the user@example.com to user@example.com:2222

Yes, I got the bookmarks back when setting the specific session port, but when doubleclick onto a bookmark, nothing happens. I expect, that the specific folder will open. It is possible to sort the bookmarks, but the bookmarks are not working.

You would have to go to registry and add the port number to the respective key. I.e. rename the user@example.com to user@example.com:2222

martin wrote:

This could happen only if your session use a non-standard port. Is that the case?

Martin, that's correct. This issue happens only for non ssh port 22 sessions. For all stored sessions with port 22 this works as expected. Is there a workaround to get back the bookmarks for the version 5.9 ?

This could happen only if your session use a non-standard port. Is that the case?

After the update from WinSCP 5.7.7 to 5.9 the existing 'Site bookmarks' for the different existing sessions are empty.

The registry key [HKEY_CURRENT_USER\Software\Martin Prikryl\WinSCP 2\Configuration\Bookmarks] contains all stored stored bookmarks.
Back to version 5.7.7 I see all stored bookmarks.