I have little experience in doing this but I did this on 10 TB OLAP database. we had around 20 data files which are residing on 4 filegroups and I made them to 4 files and 4 filegroups.

As far as I know,there is no way to empty file in chunks

Recommendations:

1) Increase the initial size of file which you dont want to delete in the file group.

2) Aviod DBCC commands while doing this.