Recently we had a similar problem and had to solve it in a different way. We had to merge two branches up to two commits, which were not the heads of either branches:
branch A: A1 -> A2 -> A3 -> A4
branch B: B1 -> B2 -> B3 -> B4
branch C: C1 -> A2 -> B3 -> C2
For example, we had to merge branch A up to A2 and branch B up to B3. But branch C had cherry-picks from A and B. When using the SHA of A2 and B3 it looked like there was confusion because of the local branch C which had the same SHA.
To avoid any kind of ambiguity we removed branch C locally, and then created a branch AA starting from commit A2:
git co A
git co SHA-of-A2
git co -b AA
Then we created a branch BB from commit B3:
git co B
git co SHA-of-B3
git co -b BB
At that point we merged the two branches AA and BB. By removing branch C and then referencing the branches instead of the commits it worked.
It's not clear to me how much of this was superstition or what actually made it work, but this "long approach" may be helpful.