How to disclose a major change in scope from orignal F31 submission
No, it's not a stain, no it doesn't matter. Not at the &quot;F&quot; level, not at the &quot;R&quot; level. All that's really important is the overall output of the project: whether you able to eventually publish papers using the funding given to you by the end of the project.
You have to complete the progress report (I believe if you do not your funding will be suspended; probably you can get the funds released if you complete it late but I don't know the details of that situation), and I would not suggest reporting that any funds have been used illegally or that you participated in research misconduct. Otherwise...it really doesn't matter for either your reputation or for you continuing to get the funds. There's a statutory requirement to submit these, and I'd suggest being truthful, but they're not going through a peer review process or anything. It's normal for projects to change, and a global pandemic is probably one of the most unassailable reasons for this.