After Hitler invaded Czechoslovakia, in March of 1939, he split the country into a Protectorate of Bohemia and Moravia, and an "independent" Slovak state. The Czechoslovak Army was disabanded, and the weapons seized for use by the Wehrmacht. The following excerpt from Wikipedia gives some idea how much army equipment Hitler confiscated from Czechoslovakia:
https://en.wikipedia.org/wiki/Munich_AgreementCzechoslovakia had fielded a modern army of 35 divisions and was a major manufacturer of machine guns, tanks, and artillery, most of them assembled in the Škoda factory in Plzeň. Many Czech factories continued to produce Czech designs until converted for German designs. Czechoslovakia also had other major manufacturing companies. Entire steel and chemical factories were moved from Czechoslovakia and reassembled in Linz (which incidentally remains a heavily industrialized area of Austria). In a speech delivered in the Reichstag, Hitler stressed the military importance of occupation, noting that by occupying Czechoslovakia, Germany gained 2,175 field cannons, 469 tanks, 500 anti-aircraft artillery pieces, 43,000 machine guns, 1,090,000 military rifles, 114,000 pistols, about a billion rounds of ammunition and three million anti-aircraft grenades. This amount of weaponry would be sufficient to arm about half of the then Wehrmacht. Czechoslovak weaponry later played a major part in the German conquests of Poland (1939) and France (1940).
The officers who were executed were no longer on active duty because the Czechoslovak Army no longer existed (except in exile) at the time these people were executed. Most of these officers were involved in underground resistance activities and they were sentenced to death and executed by Nazis for that reason.
The army was disbanded following the German takeover of Czechoslovakia in 1939. During World War II the Czechoslovak Army was recreated in exile, first in the form of the new Czechoslovak Legion fighting alongside of Poland during the Invasion of Poland and then in the form of forces loyal to the London-based Czechoslovak government-in-exile.