When deploying changes, there may be overridden config on the live site. If a block is placed, the weights on the rest of the blocks move. A view may have been modified, or a filed formatter changed.
The deployment contains config changes, and the plan is to sync config after the code is deployed. However, the live config changes need to be captured and checked into git so they can merge with the updates.
The most important thing to do is to check in these changes on the commit that is currently deployed!
That way the diff represents changes since the last deployment. This new commit can be merged into the deployment branch. Most changes should merge, but conflicts will need to be resolved.
Drush has a config:pull command that can sync config from a remote site.