Is deducting 3% of the cost of building a hotel, without the owner's knowledge, in exchange for supervising it for over two years, considered a sin requiring repentance, especially given the absence of a prior agreement on the fee and the avoidance of confronting the owner?

It is not permissible to deduct a percentage from the employer's money without his knowledge and consent. However, the supervisor has the right to demand compensation for his work and supervision if custom dictates it, even if not explicitly agreed upon, because what is customary is as binding as a condition. If there was no agreement to volunteer the supervision, and the work is such that its doer deserves compensation, then the supervisor has the right to demand it. It is not permissible to take money secretly unless the supervisor has a right that the employer denies, and he cannot obtain it except through stratagem. What was taken previously without the employer's knowledge must be returned to him, even through indirect means.