Does renaming the crontab file cause problems with the cron process?

About a week ago, I was trying to make an update to the crontab files on all of our district servers. About halfway through, I got this 'brilliant' idea to simply copy the crontab file off of a system that had been updated, and load it onto the systems that hadn't been. In order to prevent myself from clobbering the original crontab file, I renamed it to 'cron_old' before copying the updated crontab file across.

And now, for about a week, some of the servers have been missing their scheduled daily database backups. I've looked at permissions across the board for crontab file, cron.daily folder, backup job, and backup directory. As far as I can tell, the only difference between systems with working backups and those
without working backups is that the non-working ones are, so far as I can tell, those where I copied the updated crontab file over instead of attempting to update it manually. It would appear that, somehow, this is what is responsible for killing the daily backups.

The copied files were briefly routed through a windows environment; I was working on a windows-side application when the request to make the change came through, and began with putty. I used a program that maps a drive to a samba share to open the connections across which I made the actual copies.

However, there's also an hourly job run, that I check on periodically throughout the day, that hasn't failed on any of the systems as far as I can tell, and the cron.hourly folder is called one line above the call to the cron.daily folder in the crontab files. Also, the old and new crontab files differ only in the updated lines; there were no deletions, and the original system from which the updates were drawn seems to be doing fine.

What have I managed to do to the cron processes, and what is the proper way to solve the problem?

Your crontab log should reveal information about the proccess. Check it with your processes log. Double check if the cron is actually being run for the servers.

By copying the directory you might have chanched the owner or the permisions ?