Wow - thank you all so much for your input, I appreciate it more than I can possibly say. I never expected so many people to pitch in!
I'll try to clarify things and answer some of your well-pointed-out concerns.
The first thing I should note is that maybe it sounded, from my summary, as if I was closer to him than I really was. To all extents and purposes we were only ever colleagues, not even friends, and despite the long-drawn-out timeframe, we spent relatively little time interacting in real life or online. The unfriending thing must have sounded callous, but I did genuinely think at first that he wouldn't even notice I was gone.
As to the reasons - I had been chasing him quite obviously, I thought, though I always hid behind work excuses; there was some bluntness from him, and I honestly thought he was trying to push me away. (Which may still be true, but I doubt it.) I was hurt by a number of things - my hints dropping like dead stones, repeatedly...and it all built up to the point I just decided he was trying to not-so-gently warn me off. We had a casual coffee - our first time alone together - and he did all the things guys who aren't interested do...he clammed up, seemed most interested in looking at his feet, barely asked any personal questions...I thought he was either supernaturally shy, which didn't make sense given the fact that he could be quite talkative with other people...or that he was trying to let me know he didn't see me like that. And that he didn't even want to be friends.
And then I was (mis)informed by a(n un)reliable source with the big news that he actually had a girlfriend, so I thought that all made sense, and I just...
I reached the end of my rope. I thought that if he wasn't interested in me as a girl or even, apparently, as a person, he didn't need to have me on Facebook, and in fact that if he did by some miracle notice I was gone, it would be a good thing, because at least he'd know I respected his privacy and wouldn't be bothering him again, ever.
And then this colleague of mine, who I thought wanted to maintain a professional distance, started to ignore me when he saw me - for my part I avoided him out of embarrassment - and it escalated to the point where he'd talk to the person I was with as if I wasn't there at all. Yes, I should have tried to talk to him, but my embarrassment turned to hurt and then to anger and confusion. There was such tension that we needed an argument to clear it up. But you can't argue with someone who isn't talking to you, and when we finally did talk...well, I thought it was very noble of him to say goodbye after all that. Sadly I was too shocked that he was talking to me again to say anything useful. I mechanically returned his well wishes and answered his questions, and then as he left I thanked him once more for everything he had done for me.
I think I cried for two hours straight after I got back to the conference accommodation. On the train to the airport the next day I had to wear dark glasses to hide the tears that just wouldn't go away.
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When I did finally get up the courage to send him an email some months later, I made it clear that I wanted to heal the breach, and I asked if he thought we could be friends again one day in the future. He said that he didn't think there was any bad feeling between us that needed future reconciliation. There were lots of exclamation marks and he seemed happy and balanced, though surprised that I had written. He even seemed to be teasing me. I felt a fool, but I maintained my stance of trying to make amends, though I didn't have the courage to spell out why, let alone to try to refriend him.
So I didn't apologise explicitly, but I made it obvious that I wanted to restore our connection. Then I decided he probably wanted to be left alone.
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All your comments have been so helpful. Thanks so much for caring.
I do want to try to email him again - I feel like I botched my attempt to patch it up. Heck, even that was childish.
I know I owe him a proper, straightforward apology.
And I do realise that I need to be more open and less guarded.
But exactly how much I tell him, and whether I should really do it over email...from personal experience, he is alarmed easily and can overreact to smaller things than me. *cough* Though he cools down as quickly as he heats up.
Might I not scare him? I love the idea of coming clean, but I think there's a fifty-fifty chance he'll shut down...and he denied knowledge of there being anything wrong...
(Individual responses later. Thanks again, one and all!)