Sorry for the hassle when moving your project.
Alternates are handled differently in myBalsamiq (for now), as detailed here. In your case, I would suggest duplicating the alternates as new mockups from Mockups 3 for Google Drive before exporting the file to a BMMLs Zip. This way, you will see alternates mockups appearing in your myBalsamiq project too.
I’m also happy to do it for you if you’d like. Please share the related BMPR or BMMLs Zip file via firstname.lastname@example.org and I’ll send back a modified file, ready to upload in myBalsamiq.
Sorry for the convoluted process but we are getting close to having the same file format on all our products, so this shouldn’t be an issue for too long.