Despite having the mark of Ceaser I was not interested in peaceful nagotiations with him so I took Boone along, Boone had already warned me he would kill anything in a red skirt on sight, anyway, to cut a long story short, we wiped out Ceaser and his legion at the fort, we were both pleased with ourselves, but then on leaving the fort Boone was no where to be found, I got the sense from the discussions that this is where he went his own way, but had no message to confirm, was that the last I'll see of him or is this a glitch?

Any help would be appreciated.

He shouldn't just leave. Well, it depends on your conversation afterwards. Maybe he's just stuck somewhere. Try fast travelling.

If he left you based on some form of storyline driven motivation you'd lose his perk... did you lose his perk? If you didn't, try the Vault 22 companion fix. Just hop in the elevator and take it down to the bottom floor (5th? Pest Control?) and he should be there, don't ask me why... but it works, I had to do it to find Boone myself once.