You can just remove corresponding refs manually. As soon as you remove those refs, SubGit stops displaying the warning. See instructions below:
1. As repository administrator, you can remove the unsynced refs with the following commands:
a) Single ref:
cd $GIT_REPO
git update-ref -d refs/subgit/unsynced/heads/master/1
b) All unsynced refs:
cd $GIT_REPO
git for-each-ref --format="%(refname)" refs/subgit/unsynced/ | while read -r ref; do git update-ref -d "$ref"; done
c) Unsynced refs for a single branch (e.g. master):
cd $GIT_REPO
git for-each-ref --format="%(refname)" refs/subgit/unsynced/heads/master/ | while read -r ref; do git update-ref -d "$ref"; done
2. As a regular Git user from a cloned repository/working tree:
a) Single ref:
git push origin --delete refs/subgit/unsynced/heads/master/1
b) All unsynced refs:
git fetch origin +refs/subgit/unsynced/*:refs/subgit/unsynced/*
git for-each-ref --format="%(refname)" refs/subgit/unsynced/ | while read -r ref; do git push origin --delete "$ref"; git update-ref -d "$ref"; done
c) Unsynced refs for a single branch (e.g. master):
git fetch origin +refs/subgit/unsynced/heads/master/*:refs/subgit/unsynced/heads/master/*
git for-each-ref --format="%(refname)" refs/subgit/unsynced/heads/master/ | while read -r ref; do git push origin --delete "$ref"; git update-ref -d "$ref"; done
Kind regards,
Semyon Vadishev,