Generally, a current criminal case doesn’t impact expunction proceedings. The reason is that the expunction statute doesn’t give a judge discretion to deny an expunction just because you have a pending criminal case. If you’re eligible, you’re eligible.
The whole point of the expunction statute is to wipe away criminal charges that really should not have been brought in the first place. Nothing you do in the future affects whether your past case is eligible for an expunction.
That said, there is one rare exception. If you’re applying for a “discretionary expunction,” that is, an expunction where the DA’s Office has to agree to it, the DA’s Office can refuse to agree for any reason, including if you have a pending case. In that circumstance, you’re out of luck and are just going to have to wait until the statute of limitations has expired in your case.