Hi Alex,
This is the way I am thinking about your issue:
You started with the original 4 PixInsight Workspaces - because that is all PI knew about when the program started up.
You renamed these four and added another two - and then saved the project. However, PixInsight still knew about all six workspaces. Just because you had saved the project and closed PI didn't make PI 'forget' about the workspaces that you created.
So, when you restarted PI, it still knew about the six workspaces that had been created. You renamed these, and you might have even deleted one (leaving five, for example). Now, even if you 'abandoned' that processing session (i.e. you saved nothing) it doesn't affect PI - which still knows about these fibe workspaces.
Then, you re-visit your original, saved, project - which contains six workspaces, all of which have to be included within the PixInsight framework. This means that, if the six original names are all different to the five current names, you would now have eleven workspaces (five of which are effectivelyredundant). No big deal though - just delete the five unused workspaces and move on.
The easiest solution I can think of - if specific workspaces, unique to a particular project, are useful to you and the way you work - is to create a single workspace (called 'default', for example) that you always keep in the PI framework, and don't ever rename thereafter. That way, it will always be saved with any project that you save, and it will always be there if you simply open up PixInsight with no ongoing project. All that you have to then think about doing is to delete all the workspaces, except your 'default' workspace, when you are at the end of a PI session and want to close it down.
Hope this makes sense and that it helps in some way.