Don't be mistaken - when Arturs says "refresh does not copy 3rd party apps", what actually happens is "all of your 3rd party apps data is destroyed".
You will lose all 3rd party application when a sandbox refresh occurs. We were burned by this.
Atlassian uses the language "3rd party application is not copied" (https://support.atlassian.com/organization-administration/docs/what-data-is-copied-to-sandboxes/), which is technically true, dangerously ambiguous, and arguably misleading. That statement ("not copied") only tells you what doesn't happen, not what does happen. In this case, something very important does happen, but is entirely omitted. It's like saying that you didn't steal a car, but not mentioning that you did set it on fire and destroy it.
If a Sandbox refresh is about copying Production data over Sandbox data, and something is not copied from Production, it is natural to assume that the Sandbox data would be untouched (based on that language). To be explicit where Atlassian is not: During a sandbox refresh, 3rd party application is not copied from Production and is also entirely deleted.
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