It may be the case that you have inadvertently changed the model to run in “cycle time run mode”. This setting would lead a model to generate results consistent with your description (can’t turn flows into bi-flows, can’t get stocks to go negative). Cycle time is a cool capability in a lot of contexts, but not this one.
To get the model out of cycle time mode:
Enter the Run Specs dialog under the Run menu Within Run Specs, look at the upper right corner. You’ll see two radio buttons under the heading “Run Mode” Make sure that “Normal” is selected. OK your way out of the dialog.
Once you’re in “normal” run mode, you can go through each of the stocks and flows. While in the MODEL (not Map) view, open each stock and each flow. Make sure that the non-negative check box is UNCHECKED for each stock. Make sure each flow is set as a biflow.