I appreciate your patience as we work through this new system. I realize that everyone was very comfortable with the old way of doing things; unfortunately, the old way was causing the company to lose thousands of dollars. It was absolutely critical that we develop this new system at this time.
Thank you for your patience and thank you for helping us all get a hang of the new processes. We are grateful for your diligence and willingness to try new things for the sake of the company.
Sincerely,
(your name)