I've sent in a ticket about this, but has anybody else experienced this problem?
When buying any of the +X skill boosts aside from the +1 boosts (tier 0 level), are instead using the Engineering Operational Asset provisions. The normal Engineering Op-assets are also still using those as normal.
I'm going to guess that the 'Buff Provisions' are in fact supposed to be the provision for the skill boosts, but I might be wrong.
Are there other fleets out there having this same issue of 'disappearing' engineering provisions? Even if you aren't, it might be good to check and be sure.