Thanks for asking your question! I'm sorry to hear about your tax issue and I'm going to try my best to help you understand or resolve it.
What did the church do to violate their bylaws
took a vote that was against what our bylaws said we were to do
No, that would not invalidate your 501(c)(3) status
Only if your violation also violated federal tax regulations would it invalidate your designation
So, you should be good to go
Do you need anything additional?
If not, please rate my response as "excellent" using the rating feature along the bottom of your screen