So based on https://searchfox.org/mozilla-central/search?q=setSkipPausing&path=modify&case=false®exp=false it seems like the current behavior is that on any action to breakpoints (add, remove, disable or when the breakpoint is hit), the deactivate breakpoints option gets disabled.
Bug 1716505 Comment 1 Edit History
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So based on https://searchfox.org/mozilla-central/search?q=setSkipPausing&path=modify&case=false®exp=false it seems like the current behavior is that on any action to breakpoints (add, remove, disable), the deactivate breakpoints option gets disabled.