Prevent KiCAD from merging nets of two different global Labels

To speed up the process you could upload the project as a zip archive.

By the way if you want to use labels to allow the use of differing knowledge domains (which i assume you want as you have a label connected directly to a label at least once) then i suggest to have every knowledge domain in its own hierarchical sheet. In such a case do not use global labels. See Hierarchical or flat schematic design, what is best for me? (How to deal with multi page schematics?)