Sorry that we have not had time to prioritize fixing this issue! It requires changing how we manage scenarios and file locations, so it isn't something I've had a chance to focus on due to it affecting other tools. So it is best to probably manually manage scenarios on your own in this case.
Make a copy of your Scenarios/Default folder, and name it Scenarios/Scen1 or something similar. Copy your project SQLite database from the root of your project directory into this Scenarios/Scen1 folder. This makes it so Scenarios/Default and the project SQLite database in your project root are always your working files, and everything under Scenarios/Scen1 is backup. Switch between the files to load scenarios. Hope that makes sense.