Of course! Remux the DVD with muxman, putting the subtitle streams back where you want them.
Say you have streams 1, 2 and 3 and new stream 4 which you want as stream 1 (instead of the current stream 1). When you assign the streams in muxman, go to the #4 subs file when stream 1 is being muxed. Now go to stream 2 and assign the #2 subs files and the same for 3. Mux them together (don’t forget to add a celltimes.txt file for your chapters - this is easily generated when you demux with PGCDemux).
Now take the muxed project and open it in PgcEdit. Also open the original project with the menu in PgcEdit. Double click on the title you have demuxed and remuxed. Copy the subtitle CLUT. Over to the remuxed version and double click on the title and click Paste. OK and save.
In the original project, highlight the movie title and from the menu go File --> Replace VTST titles. Follow the prompts to substitute the remuxed version for the original one (select backup VOBs just in case things go amiss).
Test in a software player and burn.