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I have 2 old macs with data that needs to be moved to 1 new mac. Can I simply run migration assistant twice, moving the data into the same user account on the new mac?

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Without the source or the full functionnal specification from Apple it is impossible to give you an answer with no risk.

To clarify your question let's say your 3 Macs are named A, B and C. A being the oldest one, then B, and C the younger one.

Your question is "can I run Migration Assistant this way":

A → C
and then
B → C

I am convinced that Apple didn't take into consideration such a scheme of migration which might lead to data loss or corruption.

On the other hand, if you want to run Migration Assistant this way:

A → B
and then
B → C

I am convinced that the integration process will work correctly on B and then on C. In this case, make a full backup of B before starting.

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    But I don't think you can run migration assistant into an existing user account, it always has to make a new one. and even if it did in some way work like that, i don't think it would, for example, merge the Photo libraries of A and B. What do you think? – John Bachir Jan 4 '18 at 4:04
  • On this good point many users might ask themselves, Apple is pretty clear: you can run Migration Assistant now or later (after the automatic process at the end of a new MacOS installation). I checked it the real way and it succeded, but I didn't check it with something as important and as modified as my photo library. This is the reason I added the recommandation about backuping B, which is exactly what I did. – daniel Azuelos Jan 4 '18 at 12:01
  • @JohnBachir: I suggest you to add this very good and practical point of your problem within your original question, so as to avoid answer of people who give advice to quickly without taking into account the risk taken for the author of the question. – daniel Azuelos Jan 4 '18 at 12:06
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No. Migration won’t merge or combine accounts. Applications might work as I haven’t tried it, but user accounts can’t collide.

At best you could migrate all the users with different names then switch, export and merge by hand.

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