We examine the effect of neutrino flavor transformation by the fast flavor instability (FFI) on long-term mass ejection from accretion disks formed after neutron star mergers. Neutrino emission and absorption in the disk set the composition of the disk ejecta, which subsequently undergoes $r$-process nucleosynthesis upon expansion and cooling. Here we perform 28 time-dependent, axisymmetric, viscous-hydrodynamic simulations of accretion disks around hypermassive neutron stars (HMNSs) of variable lifetime, using a 3-species neutrino leakage scheme for emission and an annular-lightbulb scheme for absorption. We include neutrino flavor transformation due the FFI in a parametric way, by modifying the absorbed neutrino fluxes and temperatures, allowing for flavor mixing at various levels of flavor equilibration, and also in a way that aims to respect the lepton-number preserving symmetry of the neutrino self-interaction Hamiltonian. We find that for a promptly-formed black hole (BH), the FFI lowers the average electron fraction of the disk outflow due to a decrease in neutrino absorption, driven primarily by a drop in electron neutrino/antineutrino flux upon flavor mixing. For a long-lived HMNS, the disk emits more heavy lepton neutrinos and reabsorbs more electron neutrinos than for a BH, with a smaller drop in flux compensated by a higher neutrino temperature upon flavor mixing. The resulting outflow has a broader electron fraction distribution, a more proton-rich peak, and undergoes stronger radiative driving. Disks with intermediate HMNS lifetimes show results that fall in between these two limits. In most cases, the impact of the FFI on the outflow is moderate, with changes in mass ejection, average velocity, and average electron fraction of order $\sim 10\%$, and changes in the lanthanide/actinide mass fraction of up to a factor $\sim 2$.
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