Drawing an analogy, my task can be phrased like this: Evaluate a person's IQ based on several tests and examine how IQ changes over time.
I do $K$ different intelligence tests for each person several times (Day 1, Day 2,...). I need to find the factor responsible for IQ and estimate how it changes over time.
If I just needed to find IQ scores, I could do an exploratory factor analysis. Find $M$ important experiments from $K$ and calculate the loadings $L_1,L_2...L_M$.
For example, I may find these loading for the day 1 and use for other days, then I will be able to estimate the IQ dynamic. But in this case i will loose a lot of information from Day 2, and 3.
I try to formalise the problem: if i have some factor $F$ and Variables $V_1,V_2,..V_K$
$V_1 = L_1*F + N(\mu_1,\sigma_1)$
$....$
$V_K = L_K*F + N(\mu_K,\sigma_K)$
this will lead me to a usual factor analysis.
But my factors evolve during experiments
$F = w*DayN+N(\mu_d,\sigma_d)$
Could you help me to estimate $L_{1-K}$ and $w$?
Additional problem: the number of days vary between observers from 3 to 6.