Advised missing data method
In this situation the data can be analyzed in a longitudinal model using the incomplete questionnaire total scores as the outcome. In these models the missing data are handled withing the analysis. However, the longitudinal analysis method that is applied should use some form of full information likelihood estimation, to estimate the model parameters. Only in these kind of models, all the information in the model (also the incomplete information) is used to obtain the most likely parameter estimates for your data.