I think the other thread you're referring to is here:
http://www.shrapnelgames.com/cgi-bin...=008404#000001
The other thread mentions that if you give a component 0 hitpoints, it is indestructable. Also, if you make it as part of a custom racial tech tree, nobody can make their own "flag ship".
It would be quite disruptive, though, if the flag ship got lost to maintenance.
Best case scenario: have a "spare" ship already built in your "solo" system, and have it located on a sector with a warp opener. If the unthinkable happens, you could have the new flag ship into position in 1 turn (either back to the center, or back where it was when it died).