I had script deployments that I needed to delete and thought that by deleting their entries in the XML downloaded using SDF, that when I pushed the changes back to NS via SDF that those script deployment records would "magically" go away and be deleted. Alas that's not the case so I had t run an MR against the deployment internal ids to set isdeployed to false.

Depends on the project type, for SuiteApp projects it should delete the deployments

You could have marked them undeployed via SDF, but Account Customization projects are non-destructive - they don't delete anything. Different story for SuiteApps, as Michoel suggests.

Thanks but there were a lot that updating the xml by hand was gonna be tedious