Safe to Repair NTFS Drive/Partitions When Paragon Is Installed
It is safe to use Disk Utility to add/delete partitions on a drive that is partitioned in MBR or GUID. As long as paragon followed the standards, you won't have any issues.

Do note that NTFS volumes are left alone by Disk Utility so you won't be changing them - just deleting and erasing or working in the free space around them.