Problem with github synch

I have a multiply store that I want to use the same theme in.
To maintain this I want to use Github, however when I upload the the theme from git in the other stores the default pages are gone from the customizer, together with the normal front page (home page) and a few other pages.

I get a pretty extensive error log with messages like these:

Error: assets/core.css, Validation failed: Cannot overwrite generated asset 'assets/core.css'.
Error: templates/collection.clothing.json, Validation failed: Dynamic source 'block.repeater.collection.value' is type: Collection List. Setting 'collection' can only use type: Collection.
Error: templates/collection.contentcreator-wardrobe.json, Validation failed: Dynamic source 'collection.metafields.burg.content_creator.value.profile_image.value' does not exist.

Can anybody maybe give me a hint of what might be wrong?