Assembly relations not kept when project is copied

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I'm a new fusion user making an assembly at my job using the workflow described by Rob Cohee which uses the new edit in place function (https://www.youtube.com/watch?v=yPZkYSlT6FA&ab_channel=AutodeskFusion360). The workflow has worked extremely well for our application but when I used the Fusion Team website to copy the project many of the assembly contexts broke. For cooperation purposes, the main assembly consist of 2 "sub-assemblies" and then the sub-assemblies themselves contains the parts/components. In the copied project the changes made with edit in place in the main assembly do not change the parts contained in the sub-assembly, whereas they do in the original project.
The worktree in the bottom does indicate that the assembly context has been broken but I'm not sure how to fix it.