question about make.where

[dhiman009]

I am trying to impute a dataset of 1563 observations and 310 variables using random forest. (I am sorry I cannot share the data publicly)
To address the skip pattern in the survey, I first assigned a negative value to skips (the survey does not have negative entries) and created a matrix using "make.where". Then I reassigned the negative value to missing before running mice with where = 'matrix name'.
However, I could not get the missing values imputed. This may be an issue related to the seed, or the fact there are very few actual missing in some of the variables. Could anyone please suggest any material to understand the proper use of the "make.where" for addressing skip patterns.