cv::Mat imgQuery, imgTrain;
...
TRANSFORMATION_MATRIX = cv::findHomography(...)
...
cv::Mat imgTrainWarped;
cv::warpPerspective(imgTrain, imgTrainWarped, TRANSFORMATION_MATRIX, imgTrain.size());

cv::Mat imgMask = cv::Mat(imgTrain.size(), CV_8UC1, cv::Scalar(255));
cv::Mat imgMaskWarped;
cv::warpPerspective(imgMask , imgMaskWarped, TRANSFORMATION_MATRIX, imgQuery.size());

cv::Mat imgTrainWarped;
cv::warpPerspective(imgTrain, imgTrainWarped, TRANSFORMATION_MATRIX, imgQuery.size());

// now copy only masked pixel:
imgTrainWarped.copyTo(imgQuery, imgMaskWarped);

cv::warpPerspective(imgTrain, imgQuery, TRANSFORMATION_MATRIX, imgQuery.size(), INTER_LINEAR, BORDER_TRANSPARENT);