I don't think there exists simple workaround to make Bamboo picking up again deleted branches. Please take a look at the following issue: https://jira.atlassian.com/browse/BAM-12161 - there is discussion why Bamboo is behaving this way. You can consider placing your vote on that issue, so we know that re-creating deleted branches is a highly needed feature in Bamboo.
On the other hand - why re-creating manually these branches in Bamboo is not an option for you? Is it because you have multiple plans that you would have to traverse and the amount of 'create branch' buttons you would need to hit is too high? Or is it some other reason?
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