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Due to their coherence properties, dilute atomic gas Bose-Einstein condensates seem a versatile platform for controlled creation of mesoscopically entangled states with a large number of particles and also allow controlled studies of their decoherence. However, the creation of such a state intrinsically involves many-body quantum dynamics that cannot be captured by mean-field theory, and thus invalidates the most widespread methods for the description of condensates. We follow up on a proposal, in which a condensate cloud as a whole is brought into a superposition of two different spatial locations, by mapping entanglement from a strongly interacting Rydberg atomic system onto the condensate using off-resonant laser dressing [R. Mukherjee et al., Phys. Rev. Lett. 115 040401 (2015)]. A variational many-body Ansatz akin to recently developed multi-configurational methods allows us to model this entanglement mapping step explicitly, while still preserving the simplicity of mean-field physics for the description of each branch of the superposition. In the second part of the article, we model the decoherence process due to atom losses in detail. Altogether we confirm earlier estimates, that tightly localized clouds of 400 atoms can be brought into a quantum superposition of two locations about 3 μm apart and remain coherent for about 1 ms.