In the upcoming SquareLine Studio version the attention will be paid on fixing issues and improving speed of complex projects.
Until that, if you divide your project into several smaller UI-projects, and use different names for screens/widgets (e.g. a partnumber/prefix to the names), it might not be hard to have several uiXX.c and uiXX.h files beside each other. A bit of manual tweaking would still be involved though, I attached a zip-file Multi_SquareLineProject_build.zip (3.8 MB) with an example and description in README.md. There are plans for direct automatic support of this, based on an idea of a past forum question ( Option to design standalone UI elements that can be easily added to an existing UI ).