If you've used Bones v1.3 patch, I believe that resets the resawn time of the Training Hall to 1 month - it no longer resets as soon as you leave it.

2) The training hall respawns just fine in my brother's game; he's been through it a number of times. However, he went back to it last night and can't get in. He says he can see the hole but can't enter - no error message or anything, it's just like trying to walk into a wall; nothing happens. He's going to try deleting minisaves and see if that helps but it will be a few days (working overtime.)

I've no idea what's happening here, but once you've done the Training Hall once, you should be able to enter via the front door. Has he tried that?

3) When my brother went back to Lindisfarne to GM a couple of characters in Meditation, the instructor was nowhere to be found. Hard to pinpoint when he went missing; Brother can find the guy in earlier saved games, he's just not there in more recent saves. There is a character walking around under water that looks like the right one but turns out to be just a peasant. Any ideas?

Yes and no. The usual cause for a missing instructor in Lindisfarne is that they've gone to explore the sea-bottom, but there have been a few cases (I know of two) where an area simply reloads without one of the instructors. It happened to me in Frosgard with the merchant expert/master trainer. I went through the whole area with a fine-toothed comb, and he simply was not there. The only answer I can suggest is to force a respawn. Leave the region, save your game, quit the game, and delete all the minisaves that start simply "Lindisfarne". Don't delete the saves starting "Lindisfarnemonastery" or any of the other dungeons in Lindisfarne. Then return to Lindisfarne and see if he has reappeared. I've no idea why the guy vanishes, and AFAIK nobody else has come up with any ideas why, either.