The sole completed BV 238 was strafed and sunk while docked on Schaalsee. Sources differ in date, the attackers and the attack aircraft used.

According to American sources, the BV 238 V1 was destroyed while docked on Schaalsee in September 1944 by North American P-51 Mustangs of the US 361st Fighter Group. The lead Mustang, "Detroit Miss", was piloted by World War II pilot Lieutenant Urban "Ben" Drew, and another was piloted by William D. Rogers. This represented the largest aircraft to be destroyed during the war. Drew was told after the attack that he had destroyed a BV 222 Wiking. He continued to believe this was the case until he was contacted by the BBC in 1974 for a documentary and told that their research had determined that the aircraft he had destroyed was actually the BV 238 V1, undergoing flight tests at the seaplane base at Schaal Lake.

German sources, based in part on the testimony of nearby inhabitants and Blohm & Voss employees– claim that the BV 238 V1 was discovered by the RAF between April 23 and April 26, 1945. The Allies were concerned that Hitler could use it to escape to South America and so an attack followed shortly afterwards. The aircraft was attacked by Hawker Typhoons, or Hawker Tempests. Their strafing set the engines alight and the aircraft burnt and sank with only part of a wing remaining above the surface.

According to the British, the attack happened on May 4, 1945. During the strafing the back of the flying boat broke and the forward part of the plane sank into the water.

Sources:
Wikipedia - Blohm Und Voss Bv 238