There is 2 kinds of waypoints in an unit: Unit waypoint, exportable/importable as usr or so, and chart waypoint in an AT5.
As You know, RM also can export charts waypoints als shape files (for later processing in the IMC). If you look to the pic, you will find the attribute table from such a shape as sample. You can edit each field (column) with free GIS Software eg QGIS. This is not such a great problem. We have a lot small manuals for our german user on the tacklefever homepage (sample:
www.tacklefever.de/index.php?topic=4142.0). But other websites can give you much more tips for editing Attribute tables.
If you want to batch rename, it's also advantageous to use small SQL query's in the text field "VALUE" (this is the name of the waypoint in the AT5 chart). There is a lot of samples in the net, how you can query in a text field. Such query's mark all found wayoints an these now you can rename its in one step.