Hi,
I just upgraded to B4J ver 6.00 and I noticed that when I went to the visual designer, several of the layouts were missing from the layout list. These were the ones alphabetically at the end.
If I then opened them with File Open, they would appear on the list.
I'm unable to reproduce it. Tried with a project with more than 50 layouts. Note that you can always go to the Files tab (in the code editor) and click on Sync. It will update the Files tab based on the files in the Files folder.