Use diskpart to change partitions letters in MDT

In Run command line task put:
cmd.exe /c diskpart /s "%scriptroot%\changepart.txt"

Then in \Deploymentshare\Scripts folder create changepart.txt file and type into it something like:

select disk 1
online disk noerr
attributes disk clear readonly noerr
select volume 0
assign letter=F noerr
select volume 2
assign letter=D noerr
exit