OK, full time MT geek-mode on!
The only time I know that an understudy appeared in place of the main actor on a cast recording was the Original Broadway Cast album for the musical 1776 (check it out, it's one of my faves!), where Howard Da Silva, the actor who played Benjamin Franklin, was not available for the recording because he was recovering from a heart attack, so his part was done on the album by his understudy Rex Everhart. Everhart also took over the role for a while on Broadway while Da Silva recovered.
In this case, while we don't know what Dan's illness is (and it's none of our business so I wish random fans would stop asking her that on Twitter), I highly doubt it's anything as drastic as a heart attack, so I think they could wait a week or so to record a few tracks rather than replacing her with Sophie. I think Sophie is probably just recording bonus tracks, but I guess we will find out when the album is released.