Since a Secret Clearance and TS clearance are two separate things, it is unlikely the Secret Clearance would be affected. They have different standards to meet so denial of the more stringent one would not necessarily affect the lower one. However, it would be best to ask your company (if you work for a government contractor) or the government agency you work for what their interpretations and methods are. Every department, agency, etc. has their own standards.
As far as the appeal of the TS, if that is denied, you may have one more appeal opportunity to a singular high authority individual, but each agency is different, so you need to check with them. If that is also denied, you would probably have to wait one year from the time of most recent appeal denial to re-apply for a TS. That would mean starting over from scratch with a new investigator, polygraph session, filling out a new security form/application, etc. Some people who have made certain mistakes in their lives actually forego the appeal process and start the one year wait right away to distance themselves from their transgressions or resolve legal/financial issues in their life.
Depending on your finances, you should try to hire a lawyer to represent you at your appeal hearing which should be available as part of the appeal process. They are of course expensive (anywhere from $150-350/hr), but worth it in the long run, since they have the knowledge and experience with these issues and procedures. Often agreeing to a flat fee is chosen as a cheaper method. Good luck!
