I use the command:
read.otu(list=sogin.unique.phylip.fn.list, group=sogin.pick.groups)
However, it says that the number of sequences in group file contains 100000 sequences and list file contains 1434 sequences.

So I use the :
remove.seqs(accnos=sogin.unique.phylip.fn.missing.names, group=sogin.groups)
To make the two file compatible.

However, if I use the rarefaction.single() command, how can I add the abundant information in if I have changed the .groups file ?

I suspect that when you ran read.dist, you forgot to include the names file