Thanks everyone. The errors [composer] Could not find old HEAD SHA and updateReactiveCodeBlock called for codeblockId that does not exist directly point to a change tracking issue.
Confirmed: the bug also reproduces in single-root workspaces (as others noted in the thread), so it’s not specific to multi-root.
It’s the same issue as in this thread. The team is aware.
Until a fix is released, rolling back to 2.4.x and turning off “Should Auto Accept Diffs” is a solid workaround, like you already did.
I’ll update here when the fixed release is out.