Coding agent unable to resolve conflicts in their PR

[filip-be]

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Copilot Feature Area

Copilot Coding Agent

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Hi!

I have PR opened by Copilot Coding Agent.
It's been active for over a day and there was some other changes merged to main branch which resulted in checks failing on coflict resolution.

I've asked copilot to deal with that but it looks like it is not capable of doing such thing :(

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[filip-be]

Hi @omarabid!
Sure, I agree that not all conflicts can be resolved by GenAI, but this issue is not about solving all issues nor about buying yet another tool.

[ebndev]

Hi @omarabid, thanks for sharing with the community!

Unfortunately, we currently do not allow self-promotion or advertising on the Community Discussions. We want to make sure there is space for users to ask questions without overwhelming them with other conversations. Any repeat and future violations may result in a temporary or indefinite block from the Community.

We appreciate your understanding.

[hung-doan]

I ran into the same problem before. I asked Copilot to resolve the conflict, and it did a good job selecting the correct code to keep. However, the way it resolved the conflict is not what I wanted.

What I expected

• Merge the main branch into the working branch
• Resolve conflicts while preserving the original Git history from main

What actually happened

• It did not actually merge main and resolve the conflict in Git
• Instead, it compared the differences from main and manually re-applied those changes into the current working branch

This works functionally, but from Git’s perspective the conflict is still there, and I lose the Git history from main because Copilot rewrites the changes instead of performing a real merge.

I haven’t tested it yet, but I think adding some manual tweaks to the prompt/instruction to guide Copilot could make it behave as expected. Still, I hope Copilot will improve in the future and handle merges more reliably.

[sheikh-mohammad]

This is expected behavior with the Copilot Coding Agent right now.

When other commits are merged into main after the agent has already created its PR, merge conflicts can occur. Currently, the Copilot Coding Agent does not automatically rebase or resolve merge conflicts in an existing PR branch.

Why this happens

• The agent works on a snapshot of the repository at the time it starts.
• If main changes later, the agent’s branch becomes outdated.
• The agent does not continuously sync or auto-rebase.
• Conflict resolution often requires contextual judgment, which the agent may not reliably perform yet.

How to fix it

You have a few practical options:

Option 1: Manually update the branch

Rebase:

git checkout <copilot-branch>
git fetch origin
git rebase origin/main
# resolve conflicts manually
git push --force-with-lease

Or merge instead of rebase:

git checkout <copilot-branch>
git fetch origin
git merge origin/main
git push

Option 2: Close and recreate

If conflicts are complex, it may be easier to:

• Close the PR
• Ask Copilot to regenerate the changes based on the latest main

Option 3: Ask Copilot to regenerate properly

Instead of asking it to “resolve conflicts”, try prompting:

Please regenerate this PR based on the latest main branch.

This sometimes works better than asking for conflict resolution directly.

---

Suggestion for GitHub Team

It would be helpful if the Coding Agent:

• Automatically rebased before finalizing a PR
• Or detected conflicts and restarted its task on the updated base branch

Right now, manual intervention is required in these cases.

[filip-be]

Solved!
It's available right now :)
https://github.blog/changelog/2026-03-26-ask-copilot-to-resolve-merge-conflicts-on-pull-requests/