The Buddy List Migrator web tool can only migrate your private groups. Public groups won’t be displayed for migration.
Skype for Business has a buddy list size limitation of 250 contacts. If you have more than 250 contacts in your Sametime buddy list, or in a group, you won’t be able to migrate all of those contacts due to this limitation. Try choosing to migrate just the Sametime groups that you use the most, not all of them. Or choose a smaller group to migrate.
There's no undo function in the Buddy List Migrator web tool. You can delete a group from your Skype for Business desktop client by clicking on the "GROUPS" tab, then right-clicking the group name and hitting "Delete group".
There’s a couple of reasons why the number of contacts in a group wouldn't be the same after a migration. One reason, is if there was already a group named 'X' in Skype for Business with contacts in it. If that's the case then after the migration happens the group on the Skype for Business side might have more contacts than on the Sametime side. Another reason why the groups might have different numbers of contacts is if there were duplicate contacts in the Sametime side. If there are duplicate contacts, they will be de-duped on the migration. In this case, the Skype for Business side might have less contacts than the Sametime side.
This happens when the web tool can't resolve a contact in your Sametime buddy list. This might be a corrupted contact, or the user’s e-mail address might no longer be valid. You can still perform the migration, but it's a warning that this user won’t be migrated. Contacts that are not found are shown in black in your Sametime contact list.
By default, every Skype for Business contact list has two groups named 'Favorites' and 'Other Contacts'. When the web tool tries to migrate a group called 'Favorites' to Skype for Business, it says, "You can’t do that. You already have a group named Favorites!" What’s confusing is that 'Favorites' group has a display name of 'Pinned Contacts'. So when you see 'Pinned Contacts' in Skype for Business, just read it as 'Favorites'.
Theree are two things that might be happening here...