Fix broken media library- physical folder remove

I must fix one big distinguish WordPress bug: Originally my wordpress save all media as year/month. It is, physically “uploads/year/month”. For me this was nightmare: I have hundred photos but it all are individual, with it own filename.

Now I make many days work and fix my site: All images are under “uploads”-folder.

Now I must remove this year/month-folders: 2017/01…2017/02…etc, 2018/01. Simply I log in and remove this folders using ftp.

NOW problem is, inside database is hundreds broken link. When I open Media Library in WordPress all this media show broken. My site work, of course, but I want destroy this “year/month”-folder and, update database.

So, how I can update my database?
1, first I make big work and copy all my images to one folder, “uploads”.
2, then I fix all link manually. Now all my site use only and only images just in “uploads”.
This all is ok now!
3, then I remove “uploads/2017…” and “uploads/2018” (don’t worry, I can return it all).
4, now… I must fix my database. So how I can update my database. Using other plugin “Media sync” I can read folder uploads to database. But this plugin does not fix broken links inside database. So, how I can update database and remove all nonexistent media from database? Manually I can remove folders “year/month”, but how I can update database understand this? Is this possible with this your plugin?