If they could build and rebuild the Delta Flyer, they probably build quite a few torpedoes in their downtime. Maybe she put the crew of the Equinox on torpedo building duty.
The holovids always skip over Voyager's many, many detours to extract resources and manufacture replacement torpedoes. Between this, negotiating with the Borg, and massively altering the timeline, Captain Janeway is as much a popular topic of conversation outside the federation as she is within.
I'm putting my latinum on Janeway's abuse of temporal mechanics. Pretty sure our model of time, or at least the documented displacements, follow pretty closely to the many-worlds interpretation. They could've taken as much as they wanted without affecting this world's past.
There's no way in hell Voyager had a sustainable routine to last them that long and have them return so... clean...