We create a branch each time we run updates on third party software. Then after testing we merge these branches into the live site. If I start deleting these branches after they are merged will I loose the merged changes?
If you merge e.g. feature branch into master branch, and then you delete feature branch, you won't lose the merged changes from master.
Just make sure that you've merged a branch to your main branch prior to deleting it, and that there aren't any additional commits on this branch that haven't been merged yet.
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