To me, it seems this is a very persistent, long-living bug which never got around to fully being solved. Maybe it never was a priority for such a long time.. but I'm kind of hoping it would be fixed.
....
Currently, it is impossible to repair the HQ when it is partially damaged.
I don't know the exact dynamics of it - when the HQ is partially damaged you can still resupply it, and the attempt would reward you with perks upto a certain point. Then, after some supplies are out, it doesn't begin to give you any more perks, and from that point on one has to wait it out until the HQ reups.
On the other hand, when the main HQ building is fully destroyed, constant resupplying it will eventually repair it fully. The fastest reup time I've personally seen, was 6 minutes.
To me, this seems all backwards.
Hitting the HQ to damage it, is relatively much more easier than destroying it completely.
However, when the damage is partial, a damaged HQ does more harm to the country in the fact that it cannot start giving out vital information for a very long time.... whereas a completely destroyed HQ, despite total 'blindness', lasts only minutes as in most cases people actively volunteer to the effort.
So what we have, is a hard way of hitting the HQ to completely destroy it, which is less effective, and an easy method which is more effective.
To plan a strike against a HQ to completely destroy it, a well executed strike with enough buff formations at high altitudes, is required. Such efforts are usually detected in its early stages.
On the other hand, a small-scale strike is relatively easy to execute and boasts a higher success rate - as people routinely abuse the fact that they can bomb things at improper circumstances.
Unlike a large formation of buffs at high altitudes, a single buff formation can crawl NOE deep into enemy territory unnoticed for a long time. Without proper calibration they'd just stay in the F3 external view and spray the bombs in the close vicinity of the HQ. Despite the unreliable bombing method, the large payload buff formations carry will damage the HQ harshly, but usually not destroy it completely.
The risk-effect relationship seems to be all wrong in this matter. Shouldn't the people who bother to organize multiple buffs at high altitudes, risking detection and enemy interception, calibrating the bombsight and knocking the HQ completely, be rewarded with more significant results, than just one guy sneaking a plane NOE and dropping at external view and damaging the HQ only?
In that premise I request;
1) When the HQ is partially damaged, let the people be able to repair it completely.
2) When the HQ is fully down, let it be repaired upto only a certain extent(like, friendly/enemy control..). To be repaired fully people will have to just wait it out.
In other words, reverse the supply-repair situation concerning the HQ...