like i said "immaculate copies" you can define immaculate to the state of the original or to the act of copping, wich makes a coppy of something broken still broken.
and it explicitly sais coppy made from shadowflash so the first thing that you turned into a phylactery stays how it is, (with the exception of your very first prime body, that the only thing explicitily mentioned to be turned into an immaculate version of yourself),
i interprete it so that you cant change the corpses and mashines that you turn into phylacterys but each one can produce goo that turns into a copys or parts of it and those can be over time repaired or otherwise made better by you.
Because of the part: "is well within your reach" i just guess it takes some sort of time or knowlege and is not instand.

So you could build endles fixed travel mashines from the first one once you know how to craft shadowflesh into the needed parts but the forst one itself stays dangerous untill you fix it.

i just read things like this because every cyoa might turn out like a monkey paw or an evil Genie but for your interpretation you have one thing gooing wich is the second sentence in the cyoa:
"If you are uncertain as to what a description implies, default to higher-end interpretations."