First, it's normal that when you restore a .json backup file it completely replaces your existing bookmarks. To preserve existing bookmarks, before restoring a backup, use the export to HTML feature. You can import from the HTML format without losing bookmarks.

• Export Firefox bookmarks to an HTML file to back up or transfer bookmarks
• Import Bookmarks from an HTML file

Now... what to do about the corrupted .json files you recovered. Because the format is hard to read, it may be difficult to repair adequately. This has come up in other threads, and I can't recall seeing a good tool to do it. Hopefully someone else will have a suggestion other than visiting all the links in the file and bookmarking them from scratch.

Note that Windows shows a green block for folders in the Read-only box, but not a real check-mark.
Only a check mark in the Read-only box means that a folder or file is Read-only.
Windows doesn't check all the files in a folder so instead displays a green block to indicate that it is not sure.

A JSON backup is a text file, so if the file contains other character apart from readable text then the file is corrupted and Windows probably has used some clusters to store other data.
Repairing such a damaged JSON file is almost impossible (a cluster is 4 KB and you would need to fix all missing closing '}' and ']' to make Firefox pickup the remainder of the file).
The only possibility is to extract http(s) links from such a file with an editor that knows about regular expressions or use the below posted bookmarklet in Firefox.

You can try to open the JSON backup in a Firefox tab and run this JavaScript bookmarklet code.
You need to create a new bookmark and paste the JavaScript code in its location field.

javascript:(function(){var E=document.getElementsByTagName('pre')[0],T=E.innerHTML,R=/("uri":"([^"]*)")/g,i=0,r1,r2,t;t=[];while(R.test(T)){r1=RegExp.$1;r2=RegExp.$2;if(/^(https?|ftps?):/i.test(r2)){t.push('['+(i++)+']:<a href='+r2+'>'+r2+'<\/a>');}}with(window.open().document){write(t.join('<br>\n'));close();}})();

Thank you. The javascript gave me a list of my bookmarks so now all I have to do is bookmark each one of them individually. I have pages of bookmarks. I should probably do this anyway to organize them and remove the old ones.

I found a JSON file fixer at http://jsonformatter.curiousconcept.com/. I pasted my JSON file into it and ran it and it told me that I had an unexpected comma. The extra comma was clear down at the end of the file before the last closing bracket. I edited it out using Notepad, restored it and all my bookmarks are back. I should go back and check my other backups and see if they had the exact same problem. Would like to know how the extra comma got there.