Context. Mixed-variable symplectic integrators are widely used in orbital dynamics. However, they have been developed for Solar system-type architectures, and can not handle evolving hierarchy, in particular in systems with two or more stellar components. Such configuration may have occurred in the history of HD 106906, a tight pair of F-type stars surrounded by a debris disk and a planetary-mass companion on a wide orbit. Aims. We present the new algorithm ODEA, based on the symplectic algorithm Swift HJS, that can model any system (binary,...) with unstable architecture. We study the peculiar system HD 106906 as a testcase for the code. Methods. We define and compute a criterion based on acceleration ratios to indicate when the initial hierarchy is not relevant anymore. A new hierarchy is then computed. The code is applied to study the two recently evidenced fly-bys that occurred on system HD 106906, to determine if they could account for the wide orbit of the planet. Thousands of simulations have been performed to account for the uncertainty on the perturbers coordinates and velocities. Results. The algorithm is able to handle any change of hierarchy, temporary or not. We used it to fully model HD 106906 encounters. The simulations confirm that the fly-bys could have stabilized the planet orbit, and show that it can account for the planet probable misalignment with respect to the disk plane as well as the disk morphology. However, that requires a small distance at closest approach (≲0.05 pc), and this configuration is not guaranteed. Conclusions. ODEA is a very good choice for the study of non-Solar type architecture. It can now adapt to an evolving hierarchy, and is thus suitable to study capture of planets and dust. Further observations of the perturbers, in particular their radial velocity, are required to conclude on the effects of the fly-by on system HD 106906.