Give citadels baseline fuel cost and a small invulnerability fuel bay that must be refilled every day or two. Nerf void bombs dramatically, buff missiles, damage bombs, and fighters. No fuel, invulnerability turns off.
Allow attackers to anchor Citadel Invulnerability Destabilizers (CID’s) anywhere in the system, which disallow refuelling of target Citadels in the system. CID’s can target multiple Citadels, require some fuel, and can be scanned down with combat probes. If they run out of fuel, they can be scooped.
Everything else stays more or less the same as before. You can still attack the Citadel directly during its window, but you also have the option to take time to weaken it beforehand and force a fight at a time of your choosing.
Defenders can take down the CID’s, difficulty if the attackers are securing their CID’s, or easily if they aren’t.
If the Citadel is weakened and defeated by this method, let the attackers capture the Citadel instead of only blowing it up. This turns a significant percentage of the Citadel’s assets over to the capturers, similar to wormhole drops.