Yes. That is what the law says. You have to take the appropriate action to perfect your lien. If you do not do that a bonafide purchaser for value takes clear title. Deer would still have a claim against the person who signed the financing agreement, however they would not have a valid perfected lien against the tractor. OP would then be in the clear.
That is the whole purpose of having a defined procedure on how to perfect your lien. You follow it, there is a paper trail in the public record that can be searched. That way a buyer can determine if they are getting good title or clouded title, and act accordingly.
If you, as the finance company, do not follow that procedure you do not have a valid lien. You can still repo it if the original purchaser still has the tractor in his possession. If he sold it you cannot repo it. You can just sue him for the monetary damages.
EDIT: For example for $5.00 you can get a copy of a UCC lien here
Secretary of State - Business Services Division in Indiana. Just searched and the lien on my tractor came up. So don't buy my tractor unless you want to deal with CNH Capital on a repo