As I said, 1mm shouldn't make that much difference if all you changed were the hubs. Is there something else you neglected to mention in the original post, ie. a different rim?

Also, if you're running out of thread, trimming only 1mm would be a mistake, leaving you at great risk of repeating the same problem. Running out of thread means that you have at least 2mm downside room and that's if you only run out as the spokes near tension. If you run out of thread while spokes are slack you have more downside room, and I suggest you take full advantage, unless you want to continue wasting time on this build.

BTW - if it is truly borderline, and you're running out of thread as the spokes reach the top of the nipple, a cheaper, simpler solution might be to change the nipples. Nipples vary greatly in the thread overrun (beyond the top) they allow, from just about zero for Primm to as much as 3-4mm. I try to use only nipples with a decent overrun allowance so I have more upside room to target close to the top of the nipple, vs. having to aim short in the interest of more margin for error.