A storage system in one embodiment comprises a plurality of storage devices storing data pages. Each data page has a content-based signature derived from that data page. The content-based signatures are associated with physical locations storing the data pages. In response to receipt of a write input/output (IO) request that includes a data segment that is smaller than a page granularity of the storage devices, a content-based signature associated with the data segment is determined which also corresponds to a target data page stored at one of the physical locations. In response to determining the content-based signature, an inflight write count corresponding to the content-based signature is incremented. In response to a decrement request to decrement a reference count of the physical location corresponding to the content-based signature, a decrement flag corresponding to the content-based signature is set in the data structure and the decrement request is postponed.