Spay/Neuter
Are your bunnies spayed/neutered? yes
If so, for how long (for each)? They have both been fixed for over a year.

Housing
Please describe your bunnies’ current housing set-up (living together, as neighbors, etc.).

They are currently in 2 x-pens that are connected so I can separate them when I am out of the house. Before this, they were living together full time until spring fever hit and they needed to be separated and lived side by side the whole time.

Bonding background
Did you allow the bunnies to “settle-in”? yes
How would you describe your bunnies reactions towards each other (answer for each bunny): shy, scared, curious, calm, aggressive, excited, affectionate, etc.? they are very comfortable with each other. Theodore (male) is much more outgoing and Calliope (female) is much shyer but comes out of her shell when she hangs out with him! 
Have you done any “pre-bonding” (cage or litter box swaps, etc.)? yes, they have lived next to each other for the last few weeks and before that went through the entire bonding process and lived with each other for a few months.
Have you started sessions yet? yes, they have been going really well and it was pretty much love at first sight so I am just letting them spend as much time together as they can when I am home to supervise. 
How long have you been working on bonding your bunnies? I started sessions a few days ago.
How frequently do you have bonding sessions, and how long are they? They have gone for multiple hours including overnight whenever I am home.
Have you tried any stressing techniques? no because Theo isn’t scared of anything and Calliope is scared of everything.

The issue that I am having is that they seem bonded but I don’t know if they have actually worked through all of their hierarchy stuff yet. Theo will still mount every now and then which makes Calliope mad and then it leads to a chase. The most that a chase has escalated to is fur pulling but that was before they were separated and the reason that I decided to try to rebond them. I just don’t know how to get them to work through this. What are some things I can try? Would a smaller space help?