How I Updated The Virus B From 4.02 to 4.9
 

Set Reaper to 60 BPM.
Connected BCR2000 to USB, 'IN' port to Virus OUT, 'OUTA' to Virus IN.
Enabled Reaper MIDI Device BCR Port 2.
Downloaded 'chunk' files and dragged them into track 1, selected 'one track' when prompted.
Left them touching end to end.
Disable Reaper 'loop'. mode.
Left Virus in regular mode, did not go to upload mode.
Plessed play, observed, held breath.
As Reaper began to play the last chunk, the screen changed to something like, 'this is the last chunk.'
When the last file played, I pressed stop on Reaper the Virus display 'press store to commit the cahngees' or something like that. You could press something else to back out.
When I pressed store it reported that it was updating and that you shouldn't touch anything.
HTH

-UPDATE- Should mention I put the BCR in U3 mode.