I have measurement values $y_\mu$ at times $t_\mu$; the should follow a function $y(t) = f_t \, \cos (\Omega_t\cdot t - \delta)$ where $f_t, \Omega_t$ are slowly varying functions (currently I am testing with constant functions). I need to determine the frequency $\Omega$, so I select all pairs $(y_\mu, y_{\mu-1})$ with a sign change $\text{sig} \, y_\mu \neq \text{sig} \, y_{\mu-1}$ and calculate the approximate value for the zero $T_m$ using
$$ dt_m = t_m - t_{m-1} $$ $$ dy_m = y_m - y_{m-1} $$
$$ dT_m = -\frac{dt_m}{dy_m}y_m - t_m \quad (1) $$
Note that the $y_m$ defining the zeros $T_m$ form a very small subset of the original data $y_\mu$.
In order to determine $\Omega$ I use a linear fit in $n$ based on the target function
$$ T(n) = \left(n + \frac{1}{2} \right) \frac{\pi}{\Omega} + \delta t $$
(which I have to generalize once I allow for slowly varying functions $f_t, \Omega_t$)
Fitting is done using a mean squared approach. This works as expected.
The problem is to determine the error estimation for $\Omega$. In principle, this is supported by the numerical library I am using; however, I need to specify the error for each data point as input; in my case the measurement values are the $y_m$, but the input for the fit are the values $T_m$, therefore I have to specify $\Delta T_m$.
Usually, for error propagation I would use
$$ \Delta^2 T = \sum_a \left(\frac{\partial T}{\partial q_a} \right)^2 \Delta^2 q_a \quad (2) $$
where the $q_a$ are independent quantities, and $\Delta q_a$ their respective errors.
In my case this mean that for each $T_m$ I have to use $y_m, y_{m-1}$ and their respective errors $\Delta y_m, \Delta y_{m-1}$ to calculate the zero $T_m$ and its error $\Delta T_m$. But the $y_m, y_{m-1}$ are of course not independent, so $(2)$ can't be correct.
The question is, what replaces $(2)$, i.e. how do I determine the errors $\Delta T_m$, based on $(1)$?