(Phil Leckrone writes)
There is currently no tool in Paratext that does this easily. When cross references are inserted, they are placed at the beginning of a verse. However, with the parallel passage references (\r) these need to go before the verse and paragraph marks.
There was a tool for inserting expressions that could possibly be used to get the \r into the general area, but then you would still need to move it.
Another option would be to search for all \r in the base text and then manually move them.