(This is for the downloaded Mac/PC tools only, not the online tools)
Each time you download a version of the MadScience tools, you'll need to load your projects into it manually. Your project scripts are stored in a folder that you can access - and requires a simple copy (from the old version) and paste (into the new version).
On PC: MadScience_Data > StreamingAssets > NewProjectSystem
On Mac: Right click the MadScience.app, and select “show package contents” > Contents > Resources > Data > StreamingAssets > NewProjectSystem
You can either copy the whole NewProjectSystem folder, or individual projects within it. Paste them into the new tools (while the tools aren't running). Then, when you load the tools up, your project(s) will be right there for you!
Between standalone versions 2.3.5 and 2.3.6, the image filenames were all changed, so that old projects won't work if migrated as listed above. Instead…
For any project that is from a 2.3.5 or lower version, and being placed in a newer version of the tools, place the project into StreamingAssets > ImageTranslator – instead of placing it into NewProjectSystem. Any projects in the ImageTranslator folder will get converted upon launching the editor - and will get automatically moved into the NewProjectSystem folder after the conversion… at which point all the image names will be changed to the correct, new names.