We prove that the interval topology of an Archimedean atomic lattice effect algebra E is Hausdorff whenever the set of all atoms of E is almost orthogonal. In such a case E is order continuous. If moreover E is complete then order convergence of nets of elements of E is topological and hence it coincides with convergence in the order topology and this topology is compact Hausdorff compatible with a uniformity induced by a separating function family on E corresponding to compact and cocompact elements. For block-finite Archimedean atomic lattice effect algebras the equivalence of almost orthogonality and s-compact generation is shown. As the main application we obtain a state smearing theorem for these effect algebras, as well as the continuity of ⊕-operation in the order and interval topologies on them.