tv 13 free mac cannot restart on 2nd internal hd

this is my 1st post ..... ...i am using TV free v13.1 i have a mac, 10.12 my friend has a mac 10.11.....i connect via internet , no vpn or such........ .... ....his mac has 2 separate physical drives internally [no external hd], a boot drive, a backup drive - both drives are SATA and connected ....... .........a clone program [superduper!] wakes up once per day each weekday and makes sure the internal backup drive contents matches the boot hd - changes are effected and upon completion and superduper! quits boot hd ...... ,,,,,,, changes after that time are NOT saved to back hd until the next day................. i have no problem accessing his mac when it is booted normally [i.e. started from boot hd] .................some things like volume optimization CANNOT be done on the boot drive so i tell the mac to restart from the backup drive - this i do via system pref > startup disk on his mac after restart from backup hd i can no longer 'see' his mac and i am stuck i call him and he sees his desktop - reverses to startup from boot drive and after restart i can see him again ...................is there something i can do short of physically going over there to see what is going on w/ restarted setup [which i cannot see remotely]]? ....................the boot drive is faster and the backup drive [cheaper since not as fast] is there for insurance in case boot drive fails - time machine is NOT used hds are 1gb each .................thx in advance !........ps - this all used to work ok ......