Resources getting deleted on Scan?

When RapidWeaver detects missing resources in a project, if I click on remove all, will it delete the hyperlinks in the site as well? or the resources that have been uploaded?

When building or updating a site I keep the resources on the desktop so they are easy to locate. After publishing, I delete them or move them to a different folder so my desktop isn’t cluttered.

So… each time I open one of my sites to update it, I get the missing resources in this project notice. So far I have not “Removed All” because I don’t want the links to disappear, nor do I want the resources that have been uploaded to be removed. I will not use them again on other pages.

Second part, if I have an existing site with links in it but then change the option to Copy Into the Document, will all of my links change? even those without resources included? And will it copy the previously uploaded resources from the resources folder back into the project?

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