One of my four main trunks on my four year old tree grew a pretty, healthy side branch about 4" above the ground, so I have two choices:
1) Prune the main trunk itself down to 4" and let the side branch become the new main branch, which would result in a more spread out bush habit with better air flow and space between branches or...
2) Prune the side branch and have nutrients flow along its natural path up the main trunk, but have main trunks grow a bit closer together.

I wasn't sure if it was considered poor practice to train a large side branch take the place of the branch it is growing off of. Would this result in a weaker or less productive trunk? Thank you in advance for your advice!

I don't see any problem with pruning and letting the side branch grow as a main trunk.  A picture of the tree would be helpful.

It depends on where you are - Australia? Alaska? SoCal? - and what you want out of the tree, size and shape wise.  If it's not limited in spread and your tree is going to go dormant or already is dormant I wouldn't cut that main branch yet.  If it's growing then I wouldn't cut it to 4".  That side branch should be one of many fruiting branches.  From that main stem you'd want many other fruiting branches, all coming off in different directions pointing away from the center of the plant and at different heights.  Look at the nodes on the main stem and select the ones you want to grow.  Figure out the max height you want the plant and at the right time, cut it at that height.  You can treat all the main stems the same.  Don't let the fruiting branches cross.  If you want to encourage a node to grow a stem make a cut just through the cambium above the top of the node where the dormant buds are.  I wouldn't do any of this cutting until Spring when you first notice buds swelling.  But that's just my opinion.

I guess I forget to include some info! I'm in Northwest Arkansas, zone 6b/7a, my tree is dormant, this tree produces no brebas and must be pruned back to some degree to get main crop development, and unfortunately my phone isn't cooperating (maybe I can post a pic tomorrow).

This tree is potted (25 gallon) and will stay that way for a few more years at least. I'm keeping the main trunks shorter (around 16-18 inches) per a F4F article I read on pruning. I wanted to create a bush habit on a shorter tree, so my toddler can reach some of the fruit on his own (definitely a forager in the garden!).

I really wish I could find that article! If I remember correctly it started out talking about pruning of kadota fig trees in CA, had black/white pics, and it went through the pruning cuts made each year to achieve a tree with great air flow and maximized fruit production. It might not have been kadota fig trees though, since I never could find the article earlier today.

Thanks so much for the responses!

Lastly, the main and side branches are a bit close together since they are growing alongside each other. I'm concerned they may start to crowd each other as soon as they start growing/branching out this spring. Thanks again!

I think this may be the book you are looking for.   You can do a search for pruning.
https://archive.org/stream/kadotafigtreatis00clarrich#page/n7/mode/2up

YAY!!!!!!!!!! Thank you Chapman!!!!!!!!!