Since there's nothing to pay, the Bank won't accept your filing. Instead, you can submit your filings to the RDO instead.
The RDO's we have been able to interact with did say that they no longer need the hard copies if the appropriate electronic filings were done.
To be sure though, we recommend you call your RDO and confirm if they need the hard copies submitted. Most likely they'll say no need, but still better if you call.
Note that Taxumo's filings uses the same channels as eBIRForms so, to simplify matters, you can simply tell your RDO that the filings were done via eBIRForms. :)