The team had travelled to this weekend's round at the Salzburgring, but have now taken the decision to return home in an attempt to fully fix the car.
Boardman has suffered from a continuous string of setbacks and misfortunes over the opening four races of the season.
A heavy warm-up crash at Marrakech, caused by brake failure, put him out of the weekend and required his car to be re-shelled.
He was then dogged by engine issues in the following round at the Slovakiaring. Unable to qualify - he completed just one sector before a new engine misfired - he was forced to use the first race as a test, before coming through to 18th in the second.
His problems did not dissipate in Hungary, and while he was able to salvage 15th in the second race, his team have now elected to return to the factory in a bid to finally halt the run of issues.
Team principal John Boardman said: "This is not a decision we have taken lightly, but after a couple of difficult and frustrating weekends trying to fix the car in racing conditions, I think the best course of action is to make sure the car is properly sorted and back to where we had it at the start of the season.
"We have the necessary tools to get the job done, and the best place to do this is back at base."
After Austria and Russia, Portugal is the championship's only other European round before it heads to flyaway events in the Americas and Far East.
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