One of the earlier responses said you should contact a lawyer. Please, take that advice to heart and make/keep an appointment with a competent tax/non-profit attorney.
The rules are very specific about what you can and cannot do with funds coming into the non-profit, or with funds paid by your construction company to facilitate the work done by the non-profit. This is especially true when a for profit is paying a non-profit administrator to solicit funds from the public. I can assure you getting the IRS interested in co-mingling funds will do much more than simply spoil your day.
It can be worked out, but you will want an attorney to do it.
Additionally, you may want to review the by-laws of your 501-C-3 to make sure you are not required to fill the sudden vacancy. You may need to find/appoint additional persons to the Board of Directors to bring the whole thing back up to legal status.
There has been of late a great deal of interest in 501-C-3s misusing funds. The IRS is actively pursuing those suspected. It sounds like you are doing really good work. You most assuredly do not want the government upsetting that apple cart.
Crusader Rabbit