I recently installed a new version of eclipse (2018-09), and faced with this problem. So let say we have 4 opened projects A,B,C and D: 4 projects
And then we create new working set WS_01 with: View Menu (down arrow icon in package explorer) > Select working set... > New... > Java > Finish. And we add projects A and B in that set.
Then, if I select View Menu > WS_01, package explorer will show only projects A and B. The problem is, if I close project B, it will disappears from explorer. Even if I unchecked option Closed projects from View Menu > Filters ... , project B will be still missing.
But if I go back to View Menu > 1_Windows_working_set, then I can see closed folder of project B: project B is closed