A technique enables recovery of storage space trapped in an extent store from overlapping write requests associated with metadata describing volume logical storage addresses for data in the extent store. The metadata is organized as metadata entries in a multi-level dense tree metadata structure. When a level of the dense tree is full, the metadata entries of the level are merged with a next lower level of the dense tree in accordance with a dense tree merge operation. The technique may be invoked during the merge operation to process the metadata entries associated with the overlapping write requests involved in the merge operation. Processing of the overlapping write requests during the merge operation may partially overwrite extents which, in turn, may result in logical storage space being trapped in the extent store. The technique may perform read-modify-write (RMW) operations on the partially overwritten extents to recapture that trapped space.