The only time Bill calls you is to tell you that your box is currently full and that you need to change boxes in order to catch more Pokemon (because the feature that allows the PC to automatically file Pokemon into the next box -- meaning you don't need to actually change boxes every so often -- wasn't added until Ruby/Sapphire). He doesn't call you to tell you that your Pokemon has disappeared, and really, this sort of thing doesn't actually happen in normal gameplay. (I've played Crystal for years, and it's never happened to me. Not only that, but this is the first time I've heard that it happened to anyone.) If you can't find your Ho-oh, then it could mean that your Ho-oh is in another box (and you forgot that you switched boxes/placed it in another box), or you encountered a glitch that corrupted a bit of game data. Either way, Bill's most likely not the one who called you for it.
