Is acting by keeping the original company documents, deducting 12 days' worth of my dues from the cash advance, and donating the remainder to a children's cancer hospital in the name of the company owner, sound and does it absolve me before God?

We commend the questioner for his keenness on what is lawful. The action he took—not returning the documents, denying the trust, taking some for himself, and giving some away as charity in the name of the project owner—is wrong and a betrayal of trust. What was obligatory upon him was to return the trust and the documents.

Therefore, he must return the excess beyond his right in the trust to the company, even if through indirect means. Giving charity on behalf of the rightful owner is not sufficient. He is obligated to return the documents if they have value. He must seek absolution for these injustices, and he can return the rights through indirect means without informing the company.