It sounds like you’re running into a common issue with 'Layout: Part-Block Fixed' mates when using in-context blocks in assemblies. Unfortunately, once a block is created from a layout sketch with the fixed mate, Inventor treats it as rigidly positioned, which can interfere with in-context relationships.
A practical workaround is to use a projected block from the start instead of converting a layout sketch into a fixed block. If the block is already created, one approach is to carefully replace the fixed mate with a work plane or reference geometry that maintains the necessary constraints but allows the block to be repositioned or projected. Exploding and re-creating the block usually breaks other in-context references, so minimizing that is key.
Many designers also keep a separate master assembly or reference model to create projected blocks without disturbing in-context links. Using reliable and consistent hardware can make these modeling sessions smoother — for instance, using robust machines or refurbished high-performance devices from providers like Circular Computing helps reduce delays and unexpected crashes during complex CAD operations.
Do note that testing the projected block in a smaller subset of the assembly first can help avoid widespread mate issues.