Lord Theony's order for his son to stay in his room and continue to act like the Crown Prince really went to show the man's shrewdness.
Because then Lord Theony could claim to have put 'Crown Prince' on house arrest and refuse to let anyone see him, thus letting him still keep the illusion that Philips was still in the capital.
After all, other than Theony, nobody else knew that the Crown Prince was actually missing.
And this would do tremendously in his effort to take over the capital.
It would even be tens of times better than killing Philips, as Lord Theony could not only placate the loyalist nobles and officers by this, but he could also use the Crown Prince's name to issue whatever fake orders he wished, all claiming it was sanctioned by the royal family!