Wel, actually the whole point is for her not to be linked to the destruction of the sword (say, plausible deniability). That sort of rules out recovering the sword in person. She will have to be careful not to burn all the ship down, though, since it belongs to the covenant 
Ah yes, discretion.
That’s one of the reasons to employ Grogs. Get a sneaky one on your payroll
I find myself how this turned out in play.
As to affecting the sword in the hands of someone I would suggest using a second Conduit (Intangible Tunnel) effect at Touch Range and Group Target, cast through the initial Tunnel spell. Use this targeting the Grog/Person and all of their possessions as a "Group" to create a link to the sword.
Use your AC to cast Seven-League Stride to the location of the companion when he is asleep. Rather than swapping the sword for a duplicate, shave off a bit of the blade or otherwise obtain an AC of the sword, then SLStride back home. From there, start casting whatever you want on the sword.