The rules all seem to state that the petitioner can file a motion in
his own case at any time even if he still has an attorney. But is that
really the case? Would the court simply ignore the filed motion for
modification?
Generally not.
Generally, once an attorney enters an appearance, the client is allowed to communicate with the court only through that counsel until the counsel is permitted to withdraw from representing the client in a court order, usually entered on the basis of a motion to withdraw filed by the same attorney (or in the case of a substitution of one counsel for another not at issue in this fact pattern).
Indeed, even in open court, a judge will usually ignore what a client has to say when the client is represented by counsel and will ask that the client speak with his counsel to have his views expressed instead, unless the client is called as a witness by someone and then participates only as a witness.
Notwithstanding this, a court would probably recognize a motion to terminate the services of counsel filed by the client, pro se, or a motion for an extension of time or continuance explaining that some injury or similar event (e.g. counsel's death) prevented the client's counsel from acting.
Normally, the relevant procedures would be laid out in the local rules of the bankruptcy court in the judicial district in question.
A client "enters an appearance" by filing the case, but turns over authority to the attorney when the attorney enters an appearance by signing a court document of any kind (with some narrow exceptions), until the attorney is allowed to withdraw by the court. So, the client never needs to enter an appearance, the client mere needs to cease to be represented.
Notably, the fact that one attorney has entered an appearance does not mean that another attorney cannot also enter an appearance and act on behalf of a client. Withdrawal of existing counsel is not prerequisite to an entry of appearance by new counsel, even though it is prerequisite to appearing pro se in a legal matter.
Also, subject to some exceptions that should not apply (and may not be relevant in a Chapter 13 case), entities cannot represent themselves in court without a lawyer, a rule that is also frequently applied to trustees (other than the bankruptcy trustee) and executors acting in their official capacities.