This is a very common point of confusion, and you're right to be perplexed. The short answer is: no, receiving Railroad Retirement benefits does not completely "wipe out" Social Security, and it's perfectly normal for your mom to receive a 1099-SSA form.
The Railroad Retirement system is a separate federal program from Social Security, but they are very closely coordinated. The Tier I component of a Railroad Retirement annuity is designed to be the equivalent of a Social Security benefit. The two systems have an agreement. The Social Security Administration (SSA) is essentially reimbursed by the Railroad Retirement Board (RRB) for the Social Security benefits that would have been paid to railroad workers if they were under the Social Security system. This ensures the Social Security trust funds are in the same financial position they would be in otherwise. This can also happen in the other direction where the SSA with reimburse the RRB for benefits that it pays out.
Your mom's Tier I Railroad Retirement benefit is calculated based on her combined railroad and any non-railroad (Social Security) earnings. This is why her benefits are handled by the RRB, because her railroad earnings are the primary source of her retirement. Even though she receives her monthly payments from the RRB, the SSA is still involved in the background. In some cases, a beneficiary may have earned both railroad and Social Security benefits. The RRB pays out a combined benefit, and the SSA may issue a separate 1099-SSA for the portion of the benefit that is considered a Social Security payment even though it came in a combined check from RRB. This is for tax purposes.
The reason she received a 1099-SSA is likely because a portion of her combined benefit is attributable to her own Social Security earnings record (or, in some cases, a spousal or survivor benefit from someone who was under Social Security). The RRB may be paying her the combined amount in one lump sum, but for tax reporting purposes, the SSA needs to report its portion of the payment.
