Universal remotes can be programmed for most but not all of the Pioneer DVR features. Some functions would require you have a working original remote for the universal to "learn" from. The only remotes with complete Pioneer codesets available are the JP1 type of remote, currently I believe there's an inexpensive RCA variant sold at Radio Shack. Look for posts by AVS member mdavej that discuss JP1 remotes: he is incredibly knowledgeable on the subject and very helpful.
Personally, I find the universals a poor substitute unless there is no alternative. You do have alternatives, from either eBay or independent remote control vendors who still have stock of the original remotes. You don't need an exact match for the 550 remote (VXX3095
), which was actually the least popular of the Pioneer remote designs anyway. Just look on eBay or dealer sites for any Pioneer remote designed for Pioneer DVD/HDD recorders (check the listing photo to make sure it has buttons to select DVD and HDD). All Pioneer DVD/HDD remotes sold between 2003-2008 will operate all the functions of all Pioneer recorders, even if the remote is older or newer than the recorder.
The best Pioneer remote by far came with the 530/630 and has gray buttons on a silver background, VXX2967
. These are incredibly durable under hard use, easy to operate by feel in dim light, and easy to take apart and clean. The black remote VXX3288
that came with the final 560 recorder is almost as nice, followed by the "meh" white 540/550 remote with sliding cover you're familiar with.