By using other tools as you say, the problems can be easily made for Lightroom. In most cases, a re-sync of a folder (remember, the navigation screen on the left in Lightroom is NOT a file folder browse view) would resolve issues of missing files, unless of course you (your tools) moved them and you did not know where it moved them. Scary thought that.

It was not Lightroom that lost the files, but the use of tools outside of Lightroom that caused the issue.

I understand that, me, I always begin and end editing within Lightroom since it is THE database of my images, Lightroom has the capability to call any program as an external editor or plug in pretty much, so other tools can be easily added to extend Lightroom and I do that often calling GIMP myself, not a problem round tripping from Lightroom with no losses of files.

That being said, I can see why you might not like Lightroom based on your workflow, but that is your choice, not the fault of the product. Nothing wrong with your method of workflow if it gets done what you want done.

Which is why I use Bridge. Bridge has no problem with my work flow. Lightroom does. Lightroom is great if all one ever does is mess with a few pictures in Lightroom. If one does much more significant work, perhaps even multiple renditions of the same picture which then go into different file folders for different Clients, and uses different programs, too, yeah, Lightroom has a lot of problems.
I'm a big Lightroom fan for the average Joe. I, however, am much more than an average Joe so I need much more than what Lightroom can offer, or do.

Which is why I use Bridge. Bridge has no problem with my work flow. Lightroom does. Lightroom is great if all one ever does is mess with a few pictures in Lightroom. If one does much more significant work, perhaps even multiple renditions of the same picture which then go into different file folders for different Clients, and uses different programs, too, yeah, Lightroom has a lot of problems.
I'm a big Lightroom fan for the average Joe. I, however, am much more than an average Joe so I need much more than what Lightroom can offer, or do.

So you're using Bridge to catalog all your files? Not just images?

Are you talking about other Adobe programs (e.g. Dreamweaver, Illustrator, Acrobat, etc.) or are you including non-Adobe software also (e.g. word processing, email, compilers, etc.)?

I can see why you might want to include everything in your computer if you use the non-image processing programs a significant part of the time. It would help finding things other than images.

But the Adobe Bridge web page says "Bridge CC gives you centralized access to all the media assets you need for your creative projects." It seems to be concentrating on media assets, not all the other stuff. If it's a file browser based system it should be able to see everything even non-image stuff. I'm not sure why Adobe doesn't say that on their page.

That is only because NEF, like CR2 is proprietary and Adobe cannot write directly to the file, which is why a sidecar XMP file is used, or you must SAVE AS in Photoshop. Unfortunately, it is NOT automatic in Photoshop as it will default to overnight, the saving grace is ids you edit a raw file it cannot overnight by default.

I make use of Lightroom as my front end to Photoshop as well as my tool for managing and organizing my image collection.

I convert all NEF's to DNG prior to editing but after import and after deleting uneducable files, once files are DNG I eliminate the need for sidecar files since Adobe can write changes (XMP data) into the DNG files, but the raw data of the image remains untouched, the XMP changes can be backed out or removed easily within Lightroom with the click of a button.

When the image is sent from Lightroom to Photoshop, the image returned is after a save AS, so it is a fresh image, for me usually a TIFF, that gets stacked along with the original image.

The TIFF from Photoshop has all the adjustments "baked in". There is no backing them out, UNLESS the edits were done using layers for each adjustment or done as smart objects.

The basic difference is Lightroom is a parametric editor - it applies parameters to the original file to show you a different view (XMP data/XMP sidecars).

Photoshop is a pixel level editor, it changes pixels within the image, and on output you get the changed file, UNLESS you output a file that has the layers that you worked in, including an untouched background layer, or adjustments added as smart objects.

I am sure if you watch close, you will see layers, smart objects, or SAVE AS being used to preserve the original.