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I only proof via epub. PDFs are only for POD, they are horrid to proof & annotate.
I only import to Calibre for proof reading on a Kobo, but the Full Text search is good for a selection of ebooks.
I export annotations from Kobo via Calibre to KATE as plain text and have KATE session with multiple files for each project. Notepad++ is the windows equivalent.
I started with Wordstar, then clone, then my own editor, then Word 2002/XP and eventually Libre Office even before moving from Windows to Linux finally in Jan 2017.
I used to do fragments in plain text in Jota on Android, then switched to Nebo (Advanced Notebooks) on the Kobo Sage, though still Jota on the phone. Now I have Jota and Nebo on the TCL Nxtpaper11 tablet, and also Libre Office Writer to use only as a viewer. The tablet has a 256G SD Card so has every document going back to 1992 as copies of the laptop/workstation/server files. The Android Nebo is far superior to the cut down version on Kobo.
The multiple tabs/docs per project in Notepad++, then KATE on Linux is since about 2006. Also a spreadsheet to track status / revisions.
I would only use Calibre to convert to epub and manage epubs for reading on the Kobo Sage. About 700 bought ebooks since 2013 and 6000+ PD ebooks (collection started before Calibre existed). About 40 ebooks for proofing / revision and version/revision is in file name and title.
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