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Presently, the Earth Observation community is demanding applications that provide low latency and high downlink capabilities. An increase in downlink contacts becomes essential to meet these new requirements. The Federated Satellite Systems concept addresses this demand by promoting satellite collaborations to share unused downlink opportunities. These collaborations are established opportunistically and temporarily, posing multiple technology challenges to be implemented in-orbit. This work contributes to the definition of the Federation Deployment Control Protocol which formalizes a mechanism to fairly establish and manage these collaborations by employing a negotiation process between the satellites. Moreover, this manuscript presents the results of a validation campaign of this protocol with three stratospheric balloons. In summary, more than 27 federations with 63.0% of throughput were established during the field campaign. Some of these federations were used to download data to the ground, and others were established to balance data storage between balloons. These federations allowed also the extension of the coverage of a ground station with a federation that relayed data through a balloon, and the achievement of a hybrid scenario with one balloon forwarding data from a ground device. The results demonstrate that the proposed protocol is functional and ready to be embedded in a CubeSat mission.