I asked this question in the forum, but none answered, maybe you will help me.
I'm might not be the right one to respond as I live in a totally different climate.. but probably you can use my comment as a comparison
for Peruvian guava, do you mean Psidium Catleianum?
Both Coffea and Psidium are growing free in tropic (my climate) and I grow quite many species of both (Psidium and Syzigium are my favorite fruit plant genus)
Both respond well to pruning, as long as the plant is healthy, (establish root), sometimes they are quite difficult to kill here, re-sprout or suckering, both below cutting level, or just above ground.. so I think you could prune it freely. do not disturb root while it is traumatized, keep soil moist. avoid over-watering or under watering and no fertilizing until they regrow.
How ever if you worry, could also use gradual-pruning, first above the branches, with some leaves remains, then... after some month, when the lower stem respond with sprouting, prune again... wait for respond...and prune again... so on.
If you did prune it...please consider photo.. before pruning, upload here, and update after some time,... other with some situation could benefit by reading your post..