If a company is thinking that you infringed on their patented chemical formula with your Trade Secret chemical formula and sends you a "cease and desist" letter what choices do I have? Especially if I know that that my undisclosed Trade secret chemical formula is very different.
There are many options but certainly you have to do following to avoid any liabilities:-
Hire qualified attorney and get clear picture of patented claims, process, methods etc. they cover. it may seem to you that you have different product but you might be infringing other claims.
Contact a legal counsel and reply to letter based on provided deadlines.
if patent is in-fact infringing follow procedure and evaluation of re-examination or invalidation.
Go back to your books and see are you performing this activity before priority of said patent.
Get relief from local court on notice.
I am not sure but US court have closed proceedings deciding cases related to trade secrets. they are covered with confidentiality and no details are shared with other party.
Please note above comment is very much right that you require legal counsel in present case.