As the other answers indicate you don't plead guilty (or not) to indictment (or criminal information). Instead for each specific charge in an indictment you're asked whether you plead guilty or not. So if federal prosecutors somehow added additional charges to an indictment, you wouldn't automatically be pleading guilty to those as well. However prosecutors aren't able to add charges (or otherwise amend) a federal indictment after it's been made anyways. If they want to add new charges they have to get an new indictment, which would supersede the old one and invalidate any previous pleas. You'd be able to plead guilty or not knowing the all the crimes you're being accused of in that indictment.
Furthermore the principle of double jeopardy limits the ability of prosecutors to use multiple indictments with multiple trials to get around this. Basically, there can be only one trial that decides any given fact that could determine your guilt of any federal crime. So prosecutors can't try theft of trade secrets and illegal possession of trade secrets (not actually a distinct federal crime as far as I can tell) separately if both crimes require proving that you had possession of the same trade secret. Similarly they can't try you separately for lying to federal agents (making false statements) if you're being accused of lying about being in possession of the trade secret.
On the other hand if you were accused of lying about some fact not related to trade secrets offence (yet somehow still a material fact) then they could indict and try you separately. In this separate trial they wouldn't be able to use the fact that you pleaded guilty to theft of trade secrets since it wouldn't be relevant and your previous bad acts can't generally be used as evidence against you.
Finally nothing prevents a state prosecutor charging you with state crimes related the federal trade secrets crime you've pleaded guilty to. The dual sovereignty doctrine means you can be placed "in jeopardy" for the same offence in both federal and state courts, or even multiple state courts if the offence spans multiple states. However in practice the overloaded state justice systems are more than happy to leave prosecution of crimes to federal prosecutors wherever possible. They can't afford to waste resources prosecuting people who have pleaded guilty and are being punished for their crime in a federal prison. Federal prosecutors are better funded but the "Petite" policy limits their ability to prosecute an offence that's already been dealt with in a state court.