There is no built in feature for this. What we would need is to be able to export projects similar to the way backups work. There is a feature requestfor this at CRUC-681.
Currently the only way to spilt the instances, would be to make a copy of the instance by following the instructions in Migrating FishEye Between Servers.
After making the copy you would delete from both instances the projects that you did not want, for example if you had project A and B, then you would delete project A on one instance and project B on the other, so they do not overlap.
I hope that information helps.
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