Hi Maria 

1. Multishell: yes DTIPrep can deal with multishell, just make sure the data correctly converted to NRRD. See also: https://www.na-mic.org/wiki/NAMIC_Wiki:DTI:Nrrd_format

we apply DTIprep to multi-shell all the time (it's most common way to apply it). While it adjust threshold to be more forgiving for higher shells (due to the lower SNR), it's still the case that higher shell data is more likely (erroneously) removed. Thus, inspect your initial data after DTIprep and see whether you want to relax the threshold to be less strict.

2. best disable the diffusion check, just as Steven suggested

Best
Martin