Change in oxidation state due to electron-beam bombardment is quite possible. We have observed it is possible to obtain ordered oxygen vacancy in perovskite oxides due to controlled exposure to electron-beam. Removal of oxygen could lead to change in oxidation state. Although I do not know which compounds you are talking about and whether it contains oxygen or not. I think it is advisable to cross check with XRD. Check the lattice parameters before and after the bombardment with e-beam and compare with the values in literature.
Electron bombardment can have the effect of producing a "local induced stoichiometry". That is a change in the actual composition within the interaction volume due to ion migration from and to the analysed (interaction) volume. The charge imbalance thus produced can be compensated by various mechanisms, including, I suppose, the change in oxidation state. The use of different accelerating potential, beam current, spot size, dwell time and possibly a cold stage, can all contribute to changes in the observed effects, therefore giving some guidance as to the instrumental parameters to be used in order to avoid them.