Yes, the Ghosts smart group exists only on iOS and is switched on when ghost documents are found. Version 3.0.3 will also try to repair them. Did you migrate from version 2?
I also have an .mp4 affectedâŚ
In my Ghost Group is just one item, a webarchive, which canât delete.
What happens when you long-press the ghost item and choose Move to Trash?
âmove to trashâ is colored in red, when I press it, nothing happens, the file is still shown.
My files took a minute to delete, just fyi. I let it sit a minute, exited the âGhostsâ smart group, then went back in and the files were gone. I kept getting the Ghost popup in DTTG3 for a minute (almost like it kept detecting the same ones or something) but then I went into the trashes area and cleared those out and that stuck.
@eboehnisch I successfully deleted my Ghost files, (that fixed my âfailed database verificationâ error I was getting on my iPhone) and will manually restore later, but I didnât notice that my files were 0 bytes until just a few minutes ago, and have been using DT3 on my Mac all morning, adding a few files here and there to my Global Inbox.
Even with all my databases verified and repaired successfully, those files I added this morning on my Mac to my Global Inbox are not syncing to my laptop or iPhone.
Should I choose âRebuild Databaseâ?
This thread has been very useful. Iâve followed most of what others have indicated and am waiting for 3.0.3 to propagate.In a situation that might be similar to the one mentioned by @joshgibson, the four databases of mine that were affected wonât sync automatically (with the corrected ones on my Mac). When I try to switch them to do so on my iPad, I get this notice but I have no idea how to repair a database on DTTG: âFailed database verification,please repair the database.â Using the Utility commands for âfixâ and âreindex-metadataâ donât quite fit the bill (and didnât make the notice go away). Suggestions?
Wish I could help, but Iâm glad to say I donât seem to be experiencing any of these issues though I am following the threads about this news. Otherwise, happy to share and especially too since my syncs store nothing sensitive.
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Have you reenabled the automatic sync? That the files are not syncing is unrelated to this effect.
Oh, I see. I missed one crucial step. I added backups of the affected files to the databases on my Mac. Then I deleted the 0-byte documents from my DTTG databases and emptied the trash. When I tried syncâing after that, everything went swimminglyâŚ
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Sorry, how do I enable automatic sync? Iâve tried to sync manually with the sync button on all the applications across my devices, and they all appear to sync just fine â no errors or anything like that â itâs just that the handful of files I added this morning to my global inbox on my iMac are not syncing to my MacBook or iPhone.
Edit: Automatic sync was already enabled on both my macs, and I just now enabled it on my iPhone.
What I did, in DTTG, was to go to the main view that includes the Global Inbox and all other databases on the left sidebar. I clicked the icon that looks like a series of sliders. In the resulting popup, in the SYNC category, there are two options to the right of Schedule: âAutomaticâ and âManual.â Click âAutomatic.â
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That âslidersâ icon is for Settings.
Ah, gotcha. I just enabled that on my iPhone but Iâm still not seeing those files. 
Also, Automatic Sync was also enabled already on my two macs. The only device that has the files I added this morning is my iMac, and neither my MacBook (already had auto sync enabled) nor iPhone (just enabled auto sync) had those files.
I have 13 files in my Ghosts smart group, but I canât delete them. I try to Move All To Trash, but they wonât go.
Likely related: if I switch CloudKit sync to Automatic from Manual, it always switches back & warns about Ghost files.
How do I exorcise these spirit files? 
What happens when you tap Edit, then select all of them. Tap the Organize button in the lower left. Move to Trash. Does it still not work?
Donât want to start a new thread just for this quick question - is this current bug isolated to PDFs?
Unfortunately no. It can affect any document type.
Ugh, that sucks. Do you know if the issue is always (as far as you know, anyway) that it truncates the file to 0 bytes? If so then at least itâs reasonably detectable.