Once Bobbi and Mack got wind that Coulson was rebuilding S.H.I.E.L.D from the ground up, they probably figured that Fury must have left him the toolbox, and infiltrated the team to get closer to it. Now they just need to wait for the right moment to steal it from from Coulson's office and get out of town without anyone noticing they knocked Hunter unconscious. OK, that one might take some serious strategy, but it's not like there aren't plenty of other distractions on the bus.
This development could also lend itself nicely to an Agent Carter crossover, assuming (fingers crossed) it get's picked up for another season. Perhaps the toolbox was another one of Howard Stark's inventions that he gave to Peggy Carter as a gift when she started building S.H.I.E.L.D. Tony Stark may very well recognize his father's handiwork and want to take a closer look. Or it could have been another piece of confiscated goods the Howling Commandos acquired after the (first) fall of Hydra. Either way, it leaves a nice opening for us to see Hayley Atwell on screen again.
If my theory is correct, it is hard to tell what impact this development would have on Tony Stark, and by extension the rest of the Avengers team. Assuming Bobbi and Mack are working for Stark Enterprises, it seems like a huge stretch that the truth about Coulson's death and resurrection wouldn't spread. While I highly doubt they would do an Avengers/Agents of S.H.I.E.L.D crossover to address this, a girl can dream.