There might be some small inconsistencies in the JSONDB that was introduced through the manual editing but those shouldn’t impact your ability to create and modify new stuff from the UI. It might be worth exploring how you are creating and modifying things in the UI to see if there is something about the steps you are taking might be revealing a bug in how this is all managed. If there were a problem with the JSONDB severe enough to impact all your Items, it would probably be that it’s no longer syntactically correct in which case you wouldn’t be able to see any of your Items.
So I can’t answer your first question without more information. All I can say is you shouldn’t be seeing these sorts of problems frequently.
I too have had some Links become orphaned even while working through the UI but I can’t remember the steps I took when that happened. I deleted those Links from the JSONDB manually but through the REST API docs, not my hand editing the .json files. About the only thing you can’t do through the REST API docs like these is renaming an Item (because even with text configs there really isn’t a rename, there is a delete and recreate).
I’ve also recently had to change the name of some Items (I had a misspelling in one Item that needed to match some other Items for an Associated Items DP rule) and because I didn’t discover the error until I had created the rule, widgets, links, and a bunch of Item metadata it was worth the risk to edit it in JSONDB instead of recreating the Item. But this is and should only be a last resort.
I documented my procedure at OH 3 Tips and Tricks
To delete Items I find it works the best to do so from the Link. Navigate to the Link either from the Thing or from the Item and then click remove link and answer yes to also remove the Item. From the Channels page of a Thing, you have the option to remove all the links and their Items as well if you need to do it for a whole Thing.
Anyway, for your second question, probably not. It’s not so easy to achieve because that one line in a .items file is actually stored in three separate places in JSONDB, Items, Metadata, and Links. And the REST API doesn’t support “give me all the metadata on an Item” type queries so there is no way to get all the metadata. And in OH 3, the Item Metadata is really really important. Most of the work going into configuring an Item (at least in my experience) is in the metadata.