Can a new flume be installed in an existing Packaged Metering Manhole?  Maybe.  

There are a number of factors to consider:  manhole barrel diameter, manhole top style, existing flume style / size, and desired flume style / size.

One advantage of a Flume Manhole is the ability to integrate flumes that are much longer than would otherwise be able to be contained in a given manhole barrel diameter.  Any portion of the flume that won't fit inside the manhole barrel can simply extend upstream/downstream of the manhole itself...with those portions of the flume extending outside reinforced, covered, and laminated back to the manhole barrel to form a single piece watertight structure.

Parshall flumes are an excellent example of this - where even the relatively small 3" Parshall has small portions of the end adapters sticking outside the barrel of a 48" manhole. 

Now unless the existing metering manhole can be excavated and removed, any retrofit flume will have to fit inside the manhole barrel AND be able to connect to the existing flume' structure (at least where the flow enters / exists the manhole). 

Some applications won't allow the excavation / removal of the metering manhole so any retrofit flume will have to fit through the manhole's opening.  For domed top manholes this is straight forward as the top opens a full 90 degrees, but for traffic style and aluminum top manholes, the flume has to fit through the much smaller clear opening.  Don't forget that just because a flume can be passed vertically through a manhole opening that it can be rotated to a horizontal position!

If the retrofit flume won't fit through the meeting manhole opening, it may be sectioned into pieces that can fit through the opening.  Once inside the manhole, the flume can be reassembled and then installed.

If the retrofit flume is smaller than the existing flume it may be possible to configure the new flume in such a way that it nests into the existing flume.  Such dual range installations can be temporary or permanent and the flume styles of the two nesting flumes don't necessarily need to be the same.

For smaller flows where the entire original flume is contained in the metering manhole barrel, installing a new flume can be as simple as cutting the pipe connections inside the manhole, sliding the new flume into place, and then making a watertight connection with flanged ends or flexible couplings.  This approach works best when the original flume doesn't have a grout / concrete bench around it as any such benching would have to be removed to allow access to the original flume and manhole piping.

Another approach to changing out the flume in a metering manhole is to install a flume with staged end adapters.  Staged end adapters are curved to fit snugly against the barrel of a manhole without the need to connect to piping.  Naturally, the original flume / piping will have to be able to be cut out so that the piping is flush with the manhole barrel.  Once that is done, the new flume is slid into place and secured to the manhole barrel.  For certain top manhole top styles, the inlet and outlet staged end adapters may have to ship loose so that the flume can be reassembled inside the manhole.