One factor to consider, is every group out there has to think of the Clans. They ran away with a large military force (i.e. not a colonization force), spent 500 years outside the Inner Sphere, and came back with a powerful enough force to threaten the Inner Sphere.
What if other groups have learned the same lesson? What if other groups began setting plans to create deep-space colonies that are properly set up for population stability and technological research & development, and they manage to come back.
Could this have been what the super-jump drive was really for? They just have to gather enough escapees at their location, and then deep jump to their destination. The first jump is from Terra (or another source location somewhere in the Inner Sphere) to a hidden shipyard in the Oort cloud of some system. The Dropships detach and go to a second super-jump ship, while the first (using CASPAR tech) pilots itself into a CASPARized shipyard to have its core be repaired for the next wave of refugees. By using a super-jump ship, you don't need a chain of jumpships to act like breadcrumbs to lead your eemies to your new home, and searching will be harder because the potential destination is somewhere in 900 light year radius. Even then a sufficiently paranoid group might have a Command circuit in that system, but watching the destination coordinates carefully to inspect passively anyone who shows up. Do they make the proper code maneuvers? Do they make the proper running light flash pattern? Ths are ways that true followers can be separated from enemies.
The drone shipyard would be similar to the
M-9 Pavise, but with only a single shipyard for repairing super-jump vessels (maybe one or more for Dropship repairs), and a lot of spare parts to keep the space station running. Its purpose is to be hidden, not defend itself, so it will self-destruct rather than fight. Some MD might even stay behind and form a shipping company, where they drop off supplies to that station on the quiet, along with intel updates so whoever stops there and has the proper access codes will be able to get relatively current information.
Use the similar 3-key MD security that was mentioned in the Jihad books so you need three willing MD to decrypt the computers to access its memories, destination coordinates, and reset the self-destruct charge.
During the lead-up to the Jihad you might have had WoB to try setting up a command circuit of Jumpships to ferry cargo to the survey central system, and that system alone would have the final destination coordinates. They would simply send a message back to Terra that a viable location for 'Exodus Protocols' has been found. Colonization materials would have been sent the entire time, so a new colony could be set up ASAP, instead of a sudden surge of material.