Separate before you transplant and you can transplant when they are big enough you can handle them with out brusing them.Don't forget to harden them off before putting them out in the weather. YOPPER

I was transplanting my onion seedlings tonday and a neighbor who also gardens stopped by and said that I should be trimming the roots from the onion seedlings so they are short. Well I have actually seen onion seedlings sold in the stores and the roots are short so I trimmed off a good part of the roots and planted them. Now I'm concerned that I may have made a mistake in doing this and killed 100 onion plants. anyone have any thoughts?

Don't worry. Some people root prune, some don't. Some top prune, some don't.
You certainly did not kill your onion plants.......yet :)

Root pruning is to keep those sets inactive in stores. So when you transplant
your own seedlings there is no need to do that, to retard the growth.
I would (maybe) prune the top, one third, if they are lanky.

HINT: Water the seedlings real well prior to separating/xplanting.
Better yet, immerse them in some shallow water. This way they will come separate
with least resistance. Onions are perhaps the easiest to transplant and you
cannot kill them by mishandling.
One more, DO NOT xPLANT THEM TOO DEEP!!!

Cyrus Do you know the difference between a set and a seedling.
YOPPER

I Think I do know what "stets" and "seedlings" are.
The sets sold at stores, are seedlings grown commercially in some farm or greenhouse
and then pulled up, trimmed, bunched and sold. It is like a tomato seedling.
So we don't have to start from scratch.
They(sets) are usually bigger seedlings. You can buy scallions by the bunchee from store, trim the top and treat them as sets and plant them.