  YMn$_6$Sn$_6$ consists of two types of Mn-based kagome planes stacked along
$c$-axis having a complex magnetic interactions. We report a spin
reconstruction in YMn$_6$Sn$_6$ from ferromagnet (FM) into a combination of two
incommensurate spin spirals (SSs) originating from two different type of Mn
kagome planes driven by frustrated magnetic exchanges along the $c$-axis with
inclusion of Hubbard U. The pitch angle and wave vector of the incommensurate
SSs are $\sim$89.3$^{\circ}$ and $\sim$ (0 0 0.248) respectively which are in
excellent agreement with experiment. We employed an effective model Hamiltonian
constructed out of exchange interactions to capture experimentally observed
non-equivalent nature of the two incommensurate SSs which also explain FM-SS
crossover due to antiferromagntic spin exchange with correlation. We further
report the existence of topological magnon with spin-orbit coupling in
incommensurate SS phase of YMn$_6$Sn$_6$ by calculating the topological
invariants and Berry curvature profile. The location of Dirac magnon in energy
landscape at 73 meV matches with another experimental report. We demonstrate
the accuracy of our results by highlighting experimental features in
YMn$_6$Sn$_6$.
