In the early parts of 2003, Funskool returned 18 molds to Hasbro. These were many of the more desirable molds for collectors. Hasbro immediately put many of them into production and the figures appeared in the Night Force set, the 2004 Convention set, the Urban Strike set and many others. As Hasbro was gearing up molds, odd things would show up.
Below is a Muskrat figure from around 2004. While most of this mold appeared on the terrible Dreadhead figures, it was also used for the VAMP Chief Torpedo figure. But, the Muskrat head and character were never re-released. The odd thing is that his left arm is from the Hydro Viper. This implies that Hasbro re-acquired the Hydro Viper mold and, at least, tested it out. However, the Hydro Viper never returned in any Hasbro offering. Did the mold fail the production tests? Was it deemed to expensive to produce with all the Hydro Viper's accessories? Or, did Hasbro simply not think collectors would be interested in such a figure?
Considering the amount of molds that were used time and time again for the Toys R Us sets and Comic Packs, anything new would have been cool. But, none of the former Funskool molds save the Dreadnoks were released with their original gear. So, I could see how an unaccessorized Hydro Viper would not have been very well received. Muskrat, though, is a different story. There were lots of shotguns produced in the Joe Vs. Cobra era and any of them would have worked with the figure. And, while the body did get use, I don't think an appearance by the full Muskrat character would have been derided by anyone.
Those answers are likely lost to history. But, the figure below shows that Hasbro had a lot more molds available to them than they actually released during the 2000's.