When analyzing repeated binary data, the generalized estimating equations(GEE) approach produces consistent estimates for regression parameters even if an incorrect working correlation matrix is used. However, time-varying covariates experience larger changes in coefficients than time-invariant covariates across various working correlation structures for finite samples. In addition, the GEE approach may give biased estimates under missing at random(MAR). Weighted estimating equations and multiple imputation methods have been proposed to reduce biases in parameter estimates under MAR. This article studies if the two methods produce robust estimates across various working correlation structures for longitudinal binary data with time-varying covariates under different missing mechanisms. Through simulation, we observe that time-varying covariates have greater differences in parameter estimates across different working correlation structures than time-invariant covariates. The multiple imputation method produces more robust estimates under any working correlation structure and smaller biases compared to the other two methods.