By default Builder theme studio includes content creation flows that generate files in your Shopify theme, as well as modify certain theme files. This is useful for most users, since it unlocks the use of liquid targeting and server generated pages. However, this can be a pain for stores that have a dedicated engineering resource, since usually that means the theme is stored in a version control system and it is not easy to sync builder published changes with their code base.
Luckily there is a solution for this. Turning off theme page creation should solve this issue. To do this and make it so users in your organization can only create new entries for sections as well as create custom landing pages (i.e. /pages/), go to builder.io/account/organization, choose advanced settings, and then toggle the Allow full theme editing setting to false:
