Hi Selma,
The only thing that change between lesion masks and the disconnectome maps (format-wise I mean) is the values in the voxels that are continuous instead of binary. So, if you binarised your disconnectome maps they should work with AnaCOM2.
Otherwise, you can send me some of your disconnectome maps so I can have a look. Also, the log file would be useful or any error message you got.
Thanks