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Hey there. Yes, this is unfortunate. It is related to microsoft/TypeScript#17146. When merging and generating the declarations, nodes are cloned, and currently TypeScript's compiler APIs doesn't offer APIs for transforming JSDoc comments. I've tried my best at working around it, but for the time being we'll need to await movement on the related issue.
Node: v8.10.0
OS: Windows 10 1909
TypeScript: 3.7.4
rollup-plugin-ts: 1.2.1
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