What to do about a tuition reimbursement and a change in company policy?

If you had an agreement with your employer that you would receive $2000 in tuition reimbursement, then they cannot retroactively change the terms of the agreement.  The loss is on your employer.  You can voluntarily return the funds to keep peace with your employer, but they cannot garnish your paycheck without your consent.  The only time employers can take funds out of your paychecks is when authorized by law (i.e. for taxes), by court order (like child support garnishments), or by the agreement of the employee. 

This is a really unusual request by an employer-- since the situation was created by the employer.  Usually, only major employers have tuition reimbursement policies.  Before you start talking lawsuit, consider talking a bit more to the HR department and working your way up the ladder.  Sometimes, lower end "flunky managers" make bad interpretations of policy rules that HR or superiors to HR don't know about.  If this is HR trying to railroad you, go over their head.  Many companies have a 1-800 complaint line to "corporate."  This may not work, but it's cheaper than hiring an attorney.  IF they still persist and are trying to hold your job hostage, consult with an employment law attorney to write a simple demand letter for you.  If they do proceed to terminate your employment, you can file and will qualify for unemployment because the reason for the termination was on the employer, not you.  If they garnish your wages without your permission, then you would have a suit for violation of the Texas Payday Law.  However, if they don't garnish and then decide to terminate you, your remedy will probably be limited to unemployment benefits because Texas is an at-will employment state.  If you can prove that you had an employment contract with your employer, then you could file a wrongful termination suit.... but from what you're describing, it sounds like you were an at-will employee.  If you are not sure, consult with an employment law attorney.  They should be able to tell you fairly quickly what your status would be should you decide to file a suit.

Under the laws of all states in this country your employer cannot unilaterally debit money it claims that you owe it from your paycheck legally. If he or she does, you have a legitimate complaint with your department of labor as to your employer.

I suggest that the best way to try and resolve the dispute is meet with human resources at work and state your position that your applications for tuition reimbursement were submitted for repayment before the change in policy. As such, you do not owe your employer any money in return.