score:4
I believe the commenters are on the money; the mine was unimportant and became naturally flooded. My guess is:
The mine was closed in 1939 and flooded.
This sentence is badly written in a way that implies that someone flooded it in 1939. Instead it should say that in 1939, the mine was closed and became flooded.
Other questions:
Exactly when was the mine flooded?
Wikipedia implies that this was after 1939, but there's no reference. It could be any date after 1921. The 1921 date comes from this old newspaper article, which says the mine was worked on "from 1921 on".
Why was it flooded? No other Uranium mine compared to this. Was it German "Scorched Earth" practice? (Belgian Congo was owned by Belgium, although Belgium had not yet been invaded as of 1939.)
Naturally. The mine is subtropical and the nearby town of Likasi gets a fairly high amount of precipitation. According to this news article, the mine "chugged out radium for more than 20 years before the market soured and the pit was allowed to fill up with dirty, gray water".
Belgium was invaded by Germany in 1940 but large Belgian companies, like the one that owned the mine, simply relocated their headquarters to the US.
Exactly when did the US Army Corp of Engineers arrive?
Probably some time in 1943. The mine was still owned by Union Minière, who sold their uranium stocks on September 18, 1942. Only in 1943 was Edgar Sengier persuaded to sell rights to the mine, with free assistance from the US Army Corps of Engineers. Details are available in the book Uranium: War, Energy, and the Rock That Shaped the World by Tom Zoellner.
Exactly when did the mine begin producing again?
In 1943.