Just because you have applied for a patent for your invention does not necessarily mean that all of your trade secret protection is lost. A recent Fifth Circuit case explains that particular processes and know how that may relate to the invention but are not part of the disclosure remain subject to trade secret protection, as do undisclosed combinations of disclosed elements.
It is settled that publication by the USPTO constitutes a public disclosure that destroys any trade secret protection one might exist in the invention. Thus, historically once a patent issued and, after patent applications became subject to publication (year 2000), once a patent application is published, trade secret protection is lost. As a result, patent protection and trade secret protection can be mutually exclusive.
What is lost when a patent is published, however, is limited to what is disclosed. Knowledge such as how to adapt the invention to work with another device, how to care for the invention, and even how to use the invention in combination with other disclosed inventions, may remain subject to trade secret protection. Patentees would be well-served to consider what secret knowledge they have developed beyond what is disclosed in their patents, and treat that knowledge as they would any other trade secret.