I had a 120+ lb. Shep/Lab who was outside in the wet driveway when lightening struck a tree beside the driveway during a sudden summer thunderstorm, and the electric current in the air was so severe that it made my husband feel sick before he was halfway to the dog. We have no idea what kind of 'jolt' he might have taken and, of course, brought the dog inside immediately, but the incident was sufficient to make him frightfully uncomfortable with thunderstorms...but without
all of the trauma your baby is suffering.
Ziggy was quite frightened at first and just wanted to be 'pasted' to me, then always stayed near us after that incident, but gradually lost his terror of thunderstorms and fireworks, I think in part due to sleeping directly in front of the huge speakers on the bottom of our 65" rear-projection TV (we aren't 'with' the times...lol) with the volume loud enough my hearing-deficit DH could hear it during shows with loud, thunderstorm noises in them and the 'shooting' (gunfire) shows and movies, etc., that DH likes to watch. Maybe he lost suffered hearing loss...lol...but I believe he eventually became somewhat 'conditioned' to all the loud, sudden, booming sounds because there were so many and so often and without any danger or concern from us. It wasn't like we were running around shutting windows or closing doors or anything...it was just a channel change...and boom...! He'd jump, look up at me and I'd say "It's okay," and he'd lay back down on his bed...his ears would twitch for a while, then stop, and he'd be fine.
Although I never did this intentionally to 'thunderstorm' condition Ziggy, I have done 'conditioning' for other "noise" reasons which is why I am wondering if it does/would work for thunderstorms, too...maybe at least it might help reduce the terror your baby suffers. Ziggy passed last year at about 13-14 yrs. old or I would try this intentionally myself.
What I am thinking is, if you had one on those "Relaxation" CD's with thunderstorms on them and you played it over and over for her, softly at first so it is 'behind' all the regular noises as just background sound, but with regular/nice weather outside...and make sure to take her out or have windows and/or doors open, etc., so she can see...so she hears the sounds
when there is no fear factor...then increase the volume gradually until the storm sounds are prevalent but still background sound, making sure she knows the weather is fine. Be sure to play other stuff...TV, music, etc., at the same time, too, so it all gets mixed in like it would for a real storm outside. If you have a remote for your CD player, you could even start an 'indoor storm' with her outside so when she comes into the house there is already a storm is softly raging inside.
I wouldn't want to increase her fear, or traumatize her in any way, but after what happened with Ziggy, perhaps it might help if it is just the 'sound' that is bothering her.
Good luck. I so hope you are able to find a way to help your baby!