@Peter Simmons1
Please see the previous messages I have posted on this subject. What you see in the folder's properties does NOT indicate that the folder is read-only. It is only a control that will let you set or unset the read-only attribute of files within the folder. An actual read-only folder (i.e. one that would prevent you from making changes) would be set via the NTFS security permissions which you can check under the Security tab for any given file or folder.
The square blue box with a minus sign is the same as the solid black box on previous versions of Windows. You will see this on ALL folders on ALL Windows computers. It means nothing. Whether zero, some, or all files within the folder have been marked read-only, that box will look the same. It is a terrible (and obviously confusing) interface design, but it's been that way for decades. Microsoft is unlikely to change it.
In regards to the actual problem you're encountering, you said "I can't delete any folders or files that need to be cleaned up". Please provide at least one specific example with a screenshot. Then we may be able to determine the actual cause of the problem. It may be caused by OneDrive, but there are other possible reasons as well, depending on what folder we're actually talking about. It can be as simple as Explorer itself holding the folder open, which is usually solved by closing all Explorer windows.
I recommend installing Microsoft's PowerToys and enabling the tool File Locksmith. Then you can right-click a folder, select Unlock with File Locksmith and it will then tell you what process is keeping the folder open.
Also note that the confusing, redundant, folders shown in the Navigation pane can be cleaned up by simply checking/unchecking the items you want by right-clicking in the white space at the bottom of the Navigation pane or via the Folder Options dialog (scroll to the bottom). You probably will want to uncheck "Show all folders".