KTM says its "disaster" on Sunday at Brno marked the "worst day" since the start of the Austrian marque's MotoGP project.
Pol Espargaro's warm-up crash, in which the Spanish rider broke his collarbone, reduced KTM's presence to just one bike in Sunday's race for Bradley Smith.
But Smith's race ended at the third corner when he was eliminated in a three-way melee triggered by Honda wildcard Stefan Bradl.
"Today was a disaster, the worst day since we started the project," said KTM team manager Mike Leitner.
"The only positive point is that after that crash Bradley was not hurt, he's OK."
With test rider Mika Kallio out injured after a Sachsenring crash, development duties for KTM's 2019-spec bike were transferred to Smith for the Brno weekend.
Smith had two new-spec engines to use during practice and qualifying, believed to feature a counter-rotating crankshaft, but he returned to the older version for warm-up and the race.
Leitner explained that some technical niggles with the new unit convinced KTM to revert to the older engine.
"We had some electrical issues, actually," he said. "Because also we don't have the test rider [Kallio] now, so you are forced to bring some things to the race team.
"Of course not everything works out in the first moment, the situation [is] we don't have Mika, it's making our life in the races harder.
"He [Smith] went to the old engine, the spec we are using this year, because we had small question marks and we don't want to take any risks."
Leitner said it was "99%" certain KTM will field a single bike in Austria for Smith if Espargaro is unfit to race, owing to a lack of available replacements at such short notice.
Kallio had also been due to race at the Red Bull Ring as a wildcard, but will not do so as he recovers from the surgery he had on his right knee after his Sachsenring crash.
"We would like to have two bikes at the home race, but you don't find these people around the corner," Leitner said.
"The people who can ride this kind of bike, they have contracts."
Regarding which engine Smith would use in Austria, Leitner added: "Most probably [we] will not do the home race with one rider playing [with different specifications]. We will play safe."