Only during RPro installation does RPro copy legacy programs from DPro and Rapture.
For old expansion packs (whether free or paid) it depends on the installer. If the installer pre-dates RPro the old legacy paths are used. If the installer has been updated I believe it will first look for RPro then fall back to the legacy paths. This may be a problem if one has Pro but still wants to use the expansion pack in the legacy synth because the samples and the programs are in the RPro.
There is a way to consolidate everything so that DPro, Rapture and RPro use the same folders but it is a little tricky because Rapture does not handle flac files and the RPro installer removes the wav files from its multisample root. This means every time there is an update to RPro the old Rapture wav files must be copied back into the root. Other than that, all the synths can work from a common set of samples and programs. Because the program paths are hard coded directory junctions must be used to re-point them. The rest may be done with either directory junctions or registry edits.
Without consolidating the data, chances are some manual copying will be necessary to keep the legacy synths and RPro in sync.
This issue could be avoided if Cakewalk would add VST Persist Compatibility to RPro making it a drop in replacement for the legacy synths but the feature has only been used in TH3 so far. Well almost...RPro does not play ALL CSC and DPro programs correctly.