Multiple challan / delivery and single invoice

Rule 55 of CGST Rules lists out instances where delivery challan can be issued for transportation of goods without an invoice. When you are issuing invoice against those challan, I do not think there is any such requirement which says that one invoice has to be issued against one challan. 

No issue in filing return you can issue single invoice subject to issueing invoice constraints timeline

Issue of Invoice depends on the movement of Goods. In your case, you must issue invoice before movement of Goods happens.

On what basis are you issuing onlyDonly challans?

In case of supply of goods the invoice has to be issued on or before removal or delivery of goods. Rule 55 gives limited cases in which invoice can be issued subsequently. In case if invoice could not be issued at the time of removal then supplier should issue tax invoice after delivery of goods. 

No you can not issue delivery challan except below cases as per CGST rule 55. 

(a) supply of liquid gas where the quantity at the time of removal from the place of business of the supplier is not known,
(b) transportation of goods for job work,
(c) transportation of goods for reasons other than by way of supply, or
(d) such other supplies as may be notified by the Board,

Reference: https://gstindianews.info/gst-rules-in-india-central-goods-and-service-tax-rulescgst/