A.) Move these funds back into my paycheck (I understand this would come with a standard income tax rate and a penalty),
So from what I can tell from:
26 CFR § 1.132-9 - Qualified transportation fringes.
Q-14. When must the employee have made a compensation reduction election and under what circumstances may the amount be paid in cash to the employee?
Compensation reduction amounts not refundable.
Unless an election is revoked in a manner consistent with paragraph (c) of this Q/A-14, an employee may not subsequently receive the compensation (in cash or any form other than by payment of a qualified transportation fringe under the employer's plan). Thus, an employer's qualified transportation fringe benefit plan may not provide that an employee who ceases to participate in the employer's qualified transportation fringe benefit plan (such as in the case of termination of employment) is entitled to receive a refund of the amount by which the employee's compensation reductions exceed the actual qualified transportation fringes provided to the employee by the employer.
So per the tax code, any funds transferred into a qualified transportation plan can't be returned to the employee.
B.) Move these funds into my Commuter Transit account (I have this account open and is used regularly)?
From Rev. Rule 2014-32 on Qualified transportation fringes the closest clear statement about the separation of accounts is in the Situation 7 example:
Z’s smartcard includes separate accounts to separately track funds
provided directly by an employer that are available only for transit use, funds provided
directly by an employer that are only available for nontransit use (e.g., parking),
As most of the rules assign by month the compensation reduction, and focus on the fact that the account value can only be used for the specified benefit, the different categories of transit and parking have different value caps, so each type is considered "different" such that trying to transfer or co-mingle would seem to be against the rules.