[quote="v-lopez, post:6, topic:5205"]
As long as you source the original ROS workspace (say Kinetic) before building your custom distro, I believe the overlays work flawlessly.
[/quote]
I believe what @nuclearsandwich means to say is that you cannot have two install spaces active if they were not built as overlays. Your setup works, as `/opt/ros` was active while `/opt/pal` was built. But if that was not the case, there is no link between the two and `source`ing one will deactive the other.
The setup described by the OP was like that.
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