New problem with pygit2 1.5.0 KeyError object not found <commit_id>

Description of Issue

I have synchronization issues between a salt master server and gitfs through pygit2 module version 1.5.0 and with saltstack 3002.2.

Here is what I am seeing in my salt-master logs (after anonymization) :

journalctl -xn150 -f -u salt-master.service

 [ERROR   ] Exception caught while fetching gitfs remote 'ssh://git@host.domain.tld/repos/un-peu-de-sel.git': 'object not found - no match for id (3bc3ba574>
 Traceback (most recent call last):
   File "/usr/lib/python3/dist-packages/salt/utils/gitfs.py", line 2531, in fetch_remotes
     if repo.fetch():
   File "/usr/lib/python3/dist-packages/salt/utils/gitfs.py", line 820, in fetch
     return self._fetch()
   File "/usr/lib/python3/dist-packages/salt/utils/gitfs.py", line 1864, in _fetch
     fetch_results = origin.fetch(**fetch_kwargs)
   File "/usr/local/lib/python3.8/dist-packages/pygit2/remote.py", line 128, in fetch
     payload.check_error(err)
   File "/usr/local/lib/python3.8/dist-packages/pygit2/callbacks.py", line 93, in check_error
     check_error(error_code)
   File "/usr/local/lib/python3.8/dist-packages/pygit2/errors.py", line 56, in check_error
     raise KeyError(message)
 KeyError: 'object not found - no match for id (3bc3ba574e1992af38727fa67c3d6a541a2d1146)'
 [ERROR   ] Exception caught while fetching gitfs remote 'ssh://git@host.domain.tld/repos/modulefiles.git': 'object not found - no match for id (84fe4348c08ebd198>
 Traceback (most recent call last):
   File "/usr/lib/python3/dist-packages/salt/utils/gitfs.py", line 2531, in fetch_remotes
     if repo.fetch():
   File "/usr/lib/python3/dist-packages/salt/utils/gitfs.py", line 820, in fetch
     return self._fetch()
   File "/usr/lib/python3/dist-packages/salt/utils/gitfs.py", line 1864, in _fetch
     fetch_results = origin.fetch(**fetch_kwargs)
   File "/usr/local/lib/python3.8/dist-packages/pygit2/remote.py", line 128, in fetch
     payload.check_error(err)
   File "/usr/local/lib/python3.8/dist-packages/pygit2/callbacks.py", line 93, in check_error
     check_error(error_code)
   File "/usr/local/lib/python3.8/dist-packages/pygit2/errors.py", line 56, in check_error
     raise KeyError(message)
 KeyError: 'object not found - no match for id (84fe4348c08ebd198f85856077541bb5b4c97ebc)'
 [ERROR   ] Exception caught while fetching gitfs remote 'ssh://git@host.domain.tld/repos/un-peu-de-sel.git': 'object not found - no match for id (3bc3ba574>
 Traceback (most recent call last):
   File "/usr/lib/python3/dist-packages/salt/utils/gitfs.py", line 2531, in fetch_remotes
     if repo.fetch():
   File "/usr/lib/python3/dist-packages/salt/utils/gitfs.py", line 820, in fetch
     return self._fetch()
   File "/usr/lib/python3/dist-packages/salt/utils/gitfs.py", line 1864, in _fetch
     fetch_results = origin.fetch(**fetch_kwargs)
   File "/usr/local/lib/python3.8/dist-packages/pygit2/remote.py", line 128, in fetch
     payload.check_error(err)
   File "/usr/local/lib/python3.8/dist-packages/pygit2/callbacks.py", line 93, in check_error
     check_error(error_code)
   File "/usr/local/lib/python3.8/dist-packages/pygit2/errors.py", line 56, in check_error
     raise KeyError(message)
 KeyError: 'object not found - no match for id (3bc3ba574e1992af38727fa67c3d6a541a2d1146)'
 [ERROR   ] Exception caught while fetching gitfs remote 'ssh://git@host.domain.tld/repos/modulefiles.git': 'object not found - no match for id (84fe4348c08ebd198>
 Traceback (most recent call last):
   File "/usr/lib/python3/dist-packages/salt/utils/gitfs.py", line 2531, in fetch_remotes
     if repo.fetch():
   File "/usr/lib/python3/dist-packages/salt/utils/gitfs.py", line 820, in fetch
     return self._fetch()
   File "/usr/lib/python3/dist-packages/salt/utils/gitfs.py", line 1864, in _fetch
     fetch_results = origin.fetch(**fetch_kwargs)
   File "/usr/local/lib/python3.8/dist-packages/pygit2/remote.py", line 128, in fetch
     payload.check_error(err)
   File "/usr/local/lib/python3.8/dist-packages/pygit2/callbacks.py", line 93, in check_error
     check_error(error_code)
   File "/usr/local/lib/python3.8/dist-packages/pygit2/errors.py", line 56, in check_error
     raise KeyError(message)
 KeyError: 'object not found - no match for id (84fe4348c08ebd198f85856077541bb5b4c97ebc)'

Switching to a recent version of gitpython solved this issue.

Setup

My /etc/salt/master master configuration:

fileserver_backend:
  - git
gitfs_provider: gitpython
gitfs_base: master
gitfs_remotes:
  - ssh://git@host.domain.tld/repos/salt.git:
    - name: states
    - root: 'salt_states'
    - pubkey: /root/.ssh/id_rsa.pub
    - privkey: /root/.ssh/id_rsa
  - ssh://git@host.domain.tld/repos/salt.git:
    - name: reactor
    - root: 'salt_reactor'
    - pubkey: /root/.ssh/id_rsa.pub
    - privkey: /root/.ssh/id_rsa
  - ssh://git@host.domain.tld/repos/modulefiles.git:
    - name: modulefiles
    - pubkey: /root/.ssh/id_rsa.pub
    - privkey: /root/.ssh/id_rsa

ext_pillar:
  - git: 
    - master ssh://git@host.domain.tld/repos/salt.git:
      - env: base
      - name: pillar
      - root: salt_pillar
      - pubkey: /root/.ssh/id_rsa.pub
      - privkey: /root/.ssh/id_rsa

Steps to Reproduce Issue

Install saltstack 3002.2 for python3, then install pygit2 1.5.0, and configure it to use a local git repository (I am using a local gitlab server with an autosign certificate. I tried to switch to a public server but I get the same error).

Versions Report

Salt Version:
          Salt: 3002.2
 
Dependency Versions:
          cffi: 1.14.3
      cherrypy: Not Installed
      dateutil: 2.7.3
     docker-py: Not Installed
         gitdb: 2.0.6
     gitpython: 3.0.7
        Jinja2: 2.10.1
       libgit2: 1.1.0
      M2Crypto: Not Installed
          Mako: Not Installed
       msgpack: 0.6.2
  msgpack-pure: Not Installed
  mysql-python: Not Installed
     pycparser: 2.20
      pycrypto: 2.6.1
  pycryptodome: 3.6.1
        pygit2: 1.5.0
        Python: 3.8.5 (default, Jul 28 2020, 12:59:40)
  python-gnupg: 0.4.5
        PyYAML: 5.3.1
         PyZMQ: 18.1.1
         smmap: 2.0.5
       timelib: Not Installed
       Tornado: 4.5.3
           ZMQ: 4.3.2
 
System Versions:
          dist: ubuntu 20.04 focal
        locale: utf-8
       machine: x86_64
       release: 5.4.0-54-generic
        system: Linux
       version: Ubuntu 20.04 focal

Start in salt/utils/gitfs.py at fetch_remotes, fetch, and _fetch, then compare the pygit2 and GitPython paths described in the traceback. Reproduce with Salt 3002.2, pygit2 1.5.0, and the listed gitfs configuration; done means fetching the configured remotes no longer raises the reported KeyError.