im sorry to see you didnt get any replies on this.. Im also having big problems with this area. Maybe if I scour the internet and try things we can find a solution together for our problems!
Most games im trying to run with redream, (the Win CE games im trying to launch with flycast core in Retroarch - on that note, Sega rally 2 runs fine in retroarch.. others dont open at all, one opened and said "this game requires a real dreamcast bios, even tho I HAVE the bios in the system folder of retroarch (DCboot.bin). Anyways my main issue is not just the wince games but in general now many games added to the folder (the same folder that is set for redream to look for roms) are not showing up in redream.
Mostly i noticed this problem after adding some new games and converting my entire collection to .chd files to save space. The WEIRD thing is that the games that were already in my collection and working (in .gdi and some in cue/bin format, at the time) ARE still working in their chd format but many of the new games adding many of them aren't showing in redreams gui. Theoretically, when using launch box/big box, it should launch straight into the game without showing the redream gui, but as the game isn't working it launches redream instead and shows the library, where most of the many of the games I added are missing. Currently the new games I added are in chd format.. they went straight into the folder in that format. I just watched a video tutorial where a guy says the should each bein their own folder (even tho SOME games are showing up without being in their own individual folder) ..so, for the games that aren't working im gonna try that first. I will try them in their own folder as bin cue format and see if redream recognizes them, then i will try converting to chd again and see if they are still recognized. Will get back to you with any discoveries.