Actually a bootdisk has to be formatted accordingly and contain:
1. IO.SYS
2. MSDOS.SYS
3. COMMAND.COM
3. CONFIG.SYS
4. AUTOEXEC.BAT
5. HYMEM.SYS
6. DISPLAY.SYS, etc.
A simple bootdisk can be done with a dos command: format a:/sys. Or: a system can be "SYS.COM"-ed with SYS (drive letter

command.
I may have misunderstood the problem, sorry if this is the case. Tried to help.