I have a font made by Glyphs 2, and everything works fine. I updated the version of G3 last month. There are many problems when opening this file with G3 to export fonts:
An error was reported when exporting variable fonts, and I could not find a solution
I would keep it in Glyphs 3 and we fix the problems.
First, try the latest beta please. Some of the issues are already taken care of. Go to Glyphs > Preferences > Updates, activate both checkboxes and press the Update button.
Then, for the feature variations, consider switching from bracket layers to a condition feature.
And for the instances, we need to make a few settings in Font Info > Exports. I would add a Variable Font Setting, and examine your settings in the instances.