Bug confirmed. The Save PixInsight Project dialog does not preserve the state of the Include all workspaces check box across successive project write operations. Consequently, if the user loads or saves a project, creates a new workspace, and then writes the project, the newly created workspace won't be included in the project unless explicitly added to the dialog's list of workspaces.
This bug is a regression, present also in version 1.8.3. It is now fixed in the new 1.8.4 version that I am going to release in a few days.
I apologize for this error, which has caused you an important data loss. I feel very bad and hate when this happens, but unfortunately, despite all the care we try to put in our work, happens from time to time...