I don't follow this as closely as you but is this expected? What sort of historical basis is there for these people seeing themselves as separate? Beyond not liking Morales, of course.
Resources. Part of the country is much richer than the other and doesn't appreciate having its money being sent to poorer parts of the country. Not entirely unlike La Lega Nord in Italy, is my impression, though you can substitute anti-aboriginal for anti-immigrant. It's been brewing for awhile.
The country has had two capitals (Sucre and La Paz) for more than a century; regional differences aren't new. The country has also had something like 200 coups d'etat over the course of its history.
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