I'll assume you are using Javan's whenever for a starting point. This
generates a crontab file. You should be able to add a second task to the
config/schedule.rb file, re-generate and update or overwrite your existing
crontab file. I am unclear what is overwriting the schedule.rb file. As I
read the whenever documentation, whenever can modify your crontab, but you
modify schedule.rb.
I notice there are many forks of whenever, if you give us more details about
which version, whether you are using Capistrano for deployment (which will
modify schedule.rb on the production servers), etc. we may be able to help.
Jeffrey