Ok, I'll try to clarify!
First of all I remember our chat about this issue and I think I told that I couldn't make Spotlight searches on my NTFS Volumes... but the truth is that I actually can, I can just open a finder window, select any of my NTFS Volumes and search for something... then I have options to "target" my search: "This Mac", "name_of_the_NTFS_volume", "Shared". So I can select my NTFS volume and will search there without any issue (even if, as I told you, I use 3rd party software to be able to mount read/write my NTFS volumes). I don't know if this means that this Volume is indexed or not (it take a looong time to make searches)
The file that was missing in the outline after quit and re-open TN was this new file had tried to rename before... but after switching to a different external folder and coming back it was suddenly there... do its not really a big deal.
Not all the files of the outline got messed! just one! you can see it on the picture I attached... this one file was already there long before.. but the outline showed the info of the "missing file", the one I had just created! (so, at the left, in the outline "Lunes 14 -03 - 2016 "Kshitija"" is in reality the 2 first lines of that file I have just created, renamed and that was missing when opening TN again; while the lines you see at the right, in the editor, are the actual content of that file)... after I just wrote something on this file the outline got corrected!
Just a weird thing, similar to what was happening before with all the outline (also the info got messed, and was fixed when editing the file content) but this time is not related with switching from Rich mode to Markdown mode.