Assertion fails on reloading an unloaded modified document

Scenario to reproduce:

1. Open "data/samples/CLUSTALW/COI.aln".
2. Remove the COI object in the project view.
   Expected state: there is an empty document in the project view, it is marked as modified.
3. Unload the document, do not save the modifications.
4. Load the unloaded document.
   Expected state: the document is loaded, it is not marked as modified.
   Current state: an assertion fails in debug mode, the document is marked as modified even after reloading.