Splitting is easy. I have done it a number of times for various reasons. I have never attempted to maintain multiple trees. I use the split of tree for whatever reason it was created and then delete it.
Unless a lot of people end up in both trees it is not immediately obvious that there are clean up problems and then what do you do about them. There is a reason people are in both trees, they have a connection thru blood or marriage to both principle people.
If both principle people are from families that lived in the same general area for several generations you are going to eventually find connections between both sides of the family. I find them all the time in unexpected places.
It seems to me for everyone asking how to split trees there is someone wanting to know how to combine trees. Almost everyone who replies agrees splitting is much easier then combining.