So you want to use the same phone number for the desktop and the softphone?
The users currently have 2 numbers assigned to them (is my understanding). 1 of them is part of the digital line license, and the other is an additional number.

First decide which one of the number you want to keep. If it doesn't matter which one, it is easier to remove the additional number. Go to Phone System > Phone numbers > All numbers and search for 1 of the users - you should see the numbers assigned to them. 1 of the numbers would have a greyed out checkbox - this number is part of the digital line and can't be edited much here. The other number would have a checkbox which is selectable and you'll be able to delete it or move it to inventory, or reassign it.

If you like the additional numbers, and want to get rid of the digital line numbers - here are the steps:
0. (Optional) export all numbers as a spreadsheet so you know which number belongs to which user.
1. move additional numbers to inventory as described above
2. go to Phone System > Phones & Devices > User phones and select 1 of the users
3. Click on edit number and swap with the appropriate number from inventory (you can refer to the spreadsheet if you forget which number belonged to which user.