Hi, my application is damaged and I wonder if my files will be accessible if I reinstalled it ?
Yes, just install a fresh copy over it. Your data is stored in a different location.
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“Damage” is unusual and should be concerning. What caused the damage?
Hopefully whatever caused the damage did not spread beyond Scrivener and that you have backups in case that happened.
In this case, it is most likely Apple using the word rather broadly. We most often see this warning if something has gone wrong with the Mac App Store DRM and how it handles certificate expiry. When everything runs smoothly, the certificate that authenticates your purchase, or your mechanical receipt, is periodically refreshed by the App Store infrastructure. If something goes wrong, your receipt ends up looking invalid, or “damaged”. The advice given in the dialogue box to reinstall is the fix, as that forces the App Store to refresh everything.
How that happens can be a bit of a mystery. It might not even be something that went wrong on your end. There was a case a while back when Apple forgot to renew the master store certificate before it expired, and pretty much everyone had to reinstall everything. That was a fun month for support.
But, it is a blanket warning, and can mean anything that fundamentally breaks the integrity of the software, too. So that can in theory include malicious events, making it a bit of an umbrella warning worth taking seriously, where the safest course of action is to ensure you have the canonical version of the software installed.
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I tried opening Scrivener and it says it’s damaged and that I have to delete it and download it again from AppStore. But when I do that, it says i have to pay for it. I think it’s because I may have bought Scrivener from someplace else, but I can’t remember. Can anyone help me? Thank you
Download it from the Scrivener site.
If you have a licence you can enter it after installing. If you can’t find it, L&L have page to find your license.
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The “Scrivener is damaged” message is, as far as I know, exclusive to the App Store version. You shouldn’t see it from the direct sale version.
Make sure you’re logged into the App Store software with your Apple ID and look at your purchases tab.
I believe I have reviewed calls where a customer used the migration assistant and migrated apps, with them insisting they were direct purchase not App Store. BUT, it’s 3 years since I was involved in reviewing call performance and I’m 73, so perhaps the recall is not guaranteed.
I for sure don’t know my license number. I would appreciate your help. Thank you 
If you bought from the Apple Store, you won’t have a license number. Check your Apple AppStore purchase list, as @kewms suggested above.
If you bought from L&L, they will have given you a license number and they can help you recover it. See I lost my licence number, what can I do to get it back? / Purchasing and Installation / Knowledge Base - Literature and Latte Support
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What @rms said will do it!
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