ok this is going to require some backstory to understand the mechanics this will achieve.
so look at this topic: https://forum.cosmoteer.net/d/2262-the-first-true-carrier-capable-of-rebuilding-6-fighters
the general idea is that by using selective part destruction, it is possible to have a build able to spawn off fighters allowing for the creation of carriers. while returning the fighters to the carrier is impossible, it is possible to restore the carriers by simply repairing the build.
the issue is how the game determines master and child when a build is destroyed..
so the rules as i understand by testing and observation..
when you build a craft, it seems to be that the first cockpit or part you place is considered the "core peice" any peice that seperates off of this core part becomes its own craft that can only be repaired up to the parts involved when the split occurs.
in general as long as there is a cockpit in the resulting child, the entire vehicle can be rebuild and the child can be at this point considered a entirely seperate entity.
the parent cockpit which for now is still the first cockpit placed, can still repair the entire structure, including the children however the children cockpits will only be able to repair the resulting child craft.
when saving a build designed to seperate in this way, the order of building is forgotten. its no longer the first cockpit that has control. when you spawn it in as a new entity from your library or buy it in bounty hunter mode, the game redoes the calculation for which cockpit is the "Core" or "main" this calculation is currently simply a scan from top to bottom, left to right, and the top left most cockpit will always be the "core".
for example

will always have the top left ship become the "mother" as seen in this screenshot.
Edit
New info further defies the core, when a ship is spawned in, the game scans top to bottom in rows left to right, so a build like this
ends up having the top left of the 4 child fighters instead of the "escape pod" at the top become the mother as seen here
this can make the creation of a "Mothership" and "child" a bit problematic in the long term as you have to place a cockpit as high in the top left corner as you can.
so here is my suggestion.
add a Toggle switch to cockpits part menus
[Set as Primary]
when this toggle is selected, any other cockpits have the toggle turned off and that specific cockpit is always determined as the core part of the build.
IN this condition, if one were to say, set the cockpit of the bottom right ship in the previously shown screenshots it would always become the "core" which can repair the entire ship, not just the individual child.
this seems like it would be possible to implement, as when first building a craft, the first cockpit placed is considered the core, adding a ingame control that simply sets the same data initially done in a similar fashion could be used to control this feature will allow for a MASSIVE array in building options expanding the potential of building in this game without adding a specific feature to support the effect.
It would allow for easy building of "Carriers" without adding specific structures for them through clever use of game mechanics.
it could even allow for the creation of "escape pods" which players can have on a build that is set as the "core" so that it can be broken off if the ship is in danger of total annihilation for a chance to escape, and restore the build.
of course this factor could and would be highly exploitable in a multiplayer if repair of ships is allowed with the current "go into debt" system, so if you do decide to support this please keep this in mind.
thank you for your time
Ship Pictured created by Teg