OK, I did a re-test recently. It's interesting partially because I had lipid panels done at two different places from the same blood sample (well, different vials but drawn at the same time). This way we have three different sets of numbers. The numbers tagged NMR-Jan are from the first test discussed in the OP. The numbers tagged NMR-Jun are from a recent re-test, same lab (Liposcience). And the numbers tagged BHL-Jun are from the same re-test, but coming from the Berkeley Heart Lab.
What changed besides time? My diet changed a bit (not hugely), in the direction of less saturated fat and more MUFA and more carbs. A fair chunk of that additional carbs was fruits, so fructose.
Tot-C: 250 (NMR-Jan), 205 (NMR-Jun), 227 (BHL-Jun).
LDL-C: 160 (NMR-Jan), 124 (NMR-Jun), 144 (BHL-Jun).
HDL-C: 80 (NMR-Jan), 69 (NMR-Jun), 68 (BHL-Jun).
Trigs: 51 (NMR-Jan), 60 (NMR-Jun), 73 (BHL-Jun).
LDL-P: 1905 (NMR-Jan), 1611 (NMR-Jun).
HDL-P: 37.1 (NMR-Jan), 31.7 (NMR-Jun).
Small LDL-P: 149 (NMR-Jan), 608 (NMR-Jun).
ApoB: 120 (Jan), 107 (Jun), 94 (BHL-Jun).
In both cases pronounced LDL pattern A (large & fluffy).
The direction of lipid changes is a bit of a trade-off. Certainly LDL went down a noticeable amount. But HDL went down as well and trigs went up. Not up into worrisome territory, but still up.
The spike in small LDL-P is puzzling. It may be an error as the LDL size profile from Berkeley Heart Labs says that only 11% of my LDL particles are small and dense. Yes, I know that the definitions of what's "small" do not match -- I'll look into it further.
Still haven't done ApoE testing, but at the moment it does seem that my LDL is sensitive to the amount of saturated fat in my diet. N=1, of course.