The following code (based on BlockInput):
#SingleInstance,Force
applicationname=BlockInput
Run, <INSERT HERE BACKUP SCRIPT TO RUN>
BlockInput,On
counter:= <INSERT HERE THE TIME IN SECONDS TO BLOCK INPUT>
Loop,%delay%
{
ToolTip,BlockInput resumes in %counter% seconds
counter-=1
Sleep,1000
}
ToolTip
BlockInput,Off
Return
Should do what you're looking for.
<WARNING: this is untested code, be careful when testing it>