When is the best time to trim a magnolia tree?
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See if this helps! We called in an arborist for ours.
https://www.thespruce.com/the-best-time-for-pruning-magnolia-trees-2132832
http://www.treeremoval.com/trimming-and-pruning/how-and-when-to-prune-a-magnolia-tree/#.WtUU3WaZPR0
When to Prune a Magnolia Tree. For magnolias that bloom in early spring, the best time for pruning is soon after the tree has finished blooming. This can be late spring or early summer, depending on the climatic zone. Pruning too late in the season will result in fewer blossoms the following spring.
I would think you are fine to cut bottom branches.