Is the questioner obligated to return the 3,000 amount to the employer, or can he consider it against his unpaid dues of 15,000?

The contract is the law between the contracting parties unless it violates a Shariah ruling. Therefore, what the questioner and the employer agreed upon regarding conditions and salary must be fulfilled. On the other hand, it is not permissible for the employer to force the worker to waive his rights or to stipulate money in exchange for transferring sponsorship, as this is consuming wealth unjustly. If the employer forces the worker to waive his rights, the worker has the right to reclaim his due by any available means without injustice, which is known as the issue of "al-Dhafr" (taking one's right by force when the oppressor refuses to give it). Based on this, the questioner is not obliged to return the three thousand to the employer; rather, the employer is obliged to return the rest of the questioner's entitlements.