Well, if you didn't certify for unemployment for each and every one of the weeks in those 3 months after you were not working and after you filed the claim, and if you didn't appeal the initial denial within 15 days of being notified you were denied, you'll not be able in any way to recoup the unemployment benefits. Unemployment benefits, even when the claim is approved, must be initially filed for, and then each week certified for. They do not retro it back to the original date you lost the job, even if they do approve it. And of course, you'd stop certifying for weeks as soon as you returned to work. Approval for benefits has little to do with whether or not your employer fights it, and they have nothing to do with your being a disabled vet or whether or not you had additional income to live on or anything related to that.
They are based solely on whether or not you lost your job through any fault of your own. If you had, say for example, sent a threatening letter to a federal official, or had been recently arrested for some offence such as a DUI, that might be considered losing your security clearance through your own fault. If you had to jump through certain hoops to insure your on going clearance, get something done, and you didn't do it, that also might have been considered your own fault. If they just arbitrarily cancelled your security clearance, and there was no action on your part that caused it, nothing you could have done to stop it, and your employers laid you off or suspended you because you didn't have it, that sounds like something for which unemployment might very well be approved, even if you had to do it on the appeal after an initial denial.
That your employer was "fighting it" had nothing to do with whether or not you were denied on the initial decision. What did your letter telling you it was denied say, and how long ago did you receive it, and did you, within 15 days, file an appeal against this denial? If you are still within the 15 days, immediately file the appeal and ask for a hearing, even though you have returned to work.