I had this problem (I believe) for me it was down to the configuration and explanation of the snapvault setup. It states
"New-NaSnapvault /vol/vol0/svsec dunn /vol/vol0/svpri"
This is a qtree to qtree level snapvault relationship. It appears that if you do not do this this way it excepts the command but adds an extra slash on the source volume and therefore cannot update the relationship. I had this problem because I was doing volume to qtree relationships. for example
"New-NaSnapvault -SecondaryPath "/vol/sv_destinationVol/Qtree1" -PrimarySystem "Filer02" -PrimaryPath "/vol/SourceVol"
I ended up with
/vol/SourceVol// Filer01:/vol/sv_destinationVol/Qtree1
after running the snapvault destinations command. Notice the double slash after the SourceVol
I fixed this by adding a slash and hyphen after the volume as instructed when doing this from command line. for example:
"New-NaSnapvault -SecondaryPath "/vol/sv_destinationVol/Qtree1" -PrimarySystem "Filer02" -PrimaryPath "/vol/SourceVol/-"
This made the snapvault relationships look correct and allowed updating.
Hope this helps