Very strange, although not unheard of. If you check some older threads on this forum you can find others who have had the same problem as you. Some followers seems to disappear when you tell them to wait or leave. No one seems to know what causes this problem or how to solve it. It is possible that this is a bug (since arcanum is loaded with them) and that it causes the followers to disappear from the game instead of return to their point of origin.
How long have you been waiting for him btw? I dont know about dismissed followers but if you tell them to wait most of them will remain in that area for a week or two (while the impatient Geoffrey will leave right away). I remember that when i told Magnus to leave while being in the boil he was back at schylers after a couple of days. Perhaps it takes him longer to return if you leave him far from Tarant (since walking all the way there will take a while).
Finally: You know that you dont need Magnus for the Iron Clan quest? You get some extra dialogue from having him in the party (and more still if you have Loghaire aswell) but the entire quest can be done without him (i just did, when playing an evil character on top of that
).
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