The missing assets message will not show again after saving without it and reloading your city

BEFORE TRYING THIS, CREATE A BACKUP OF YOUR SAVED MAP AND PUT IT ON YOUR DESKTOP IN CASE YOU DO THIS WRONG OR I DON'T EXPLAIN THIS WELL ENOUGH. ;)

ALSO BACKUP ANY PROP ANARCHY/EML CONFIG FILES ON YOUR DESKTOP IN CASE YOU NEED TO USE THAT PART OF THIS ATTEMPTED FIX.

You could first try using MOVE IT'S feature to SELECT EVERYTHING and use the multi-select tool to grab it... BUT don't delete right away IF it actaully selects the invisible item...
Sometimes things get stuck in some kind of limbo where you cannot see the asset but it's there.
It's a rare problem but if you're using the more modern prop anarchy set of tools or that extended managers library mod, it happens occasionally.

If you do see the item selected with the move it option selected, then DON'T delete it right away. Try using the select tool to grab just that asset if you can so when using the multi-select tool in move it you can grab only that asset and drag the whole map to see if there's other instances of that asset, then delete them all.

Then close and reopen your steam and your game in the proper order without doing QUICK to desktop options if you have them

Sometimes you will even have to unsub that prop anarchy and eml mod then delete the config files for them to fix this but do that as a last resort.

Make sure the INVISIBLE item if that's what it is, is the only thing you select because that tool is very powerful and literally will grab everything including pipes/pathways inside assets...