Hi Joe..Pruning won't harm your citrus..the only disadvantage is, by doing so, you'll upset flowers/fruiting. Are your trees bushes or standards?
They really shouldn't require stakes..I imagine they need more sun than they're getting. What type of light are they kept in? If indoors, what directions do windows face?
They prefer south or west exposure.
Otherwise, there's no harm in pruning. Then once you set outside, start with shady to medium light, gradually setting in full sun..Good luck, Toni

Citrus are very sensitive to repotting and changes in location. Once they're established and healthy, they're pretty resilient. If they're long and leggy because you're getting new growth, you can prune away. On the other hand if your plants have not yet rebounded, I would wait until they have acclimated to their new digs and show new growth before pruning.

Having said that, I'm impressed that any of you are able to successfully grow fruiting citrus indoors. In Southern California in the ground, they grow like weeds, but are tricky outside in a pot. Unless its a green house, inside in a pot must be very difficult.

I agree with Wfspath, you should wait before pruning..Only if foliage/stems don't improve would I prune..pruning is a last resort.

Wf, it IS difficult growing citrus indoors..You guys up west and south are sooo very lucky living in the perfect climate. It's not bad when citrus are outside enjoying sun, fresh air, humiidty, but once we bring inside..dry, stale air, lack of light, can be a problem. Insects are on the hunt looking for a dry, wet soiled tree to munch on..and it's not like we can set trees outside when it's -4..LOL..don't think they'd appreciate the fresh air then..So, be thankful you live in a nice area..Toni