Vito, the fix for your problem is a pain, but it’s not difficult, just time consuming. That said, you don’t need to be sitting in front of your Mac while it’s going on. If it were me, I would definitely move to Mojave. It’s a big step forward from Sierra, for the system (the under-the-hood stuff) and as Walter points out, you move to APFS, which is a vastly more efficient and safer format. (There is a weirdness if you work with networked Macs which are too old to be upgraded, because they can’t see the APFS files, but there are workarounds). Unlike so many system ‘upgrades’ of the past, you won’t find your Mac getting slower and may in fact find it’s a bit faster. I always recommend to people to use Time Machine, but it may not be good for everything … Personally, I’ve been working with ~100 megapixel image files since around 2007, so I have some experience of TM’s unsuitability for large files. 
So, I exclude ALL my work files, which are all in there own top-level folder which I simply call, ‘work_inProgress’. TM does everything else and most importantly, the Mac system itself. I use Chronosync for these work files and it does a great job. If you want to use a networked backup system (which I do) it’s the only game in town really, because of the way ChronoAgent works. Your backups are also automatically verified because they’re across ethernet. So it’s more reliable than copying from one disk to another. (TM is also thoroughly verified). I’ve used Chronosync for many years and wouldn’t hesitate to recommend it. I used CCC prior to that and it was also very good, but when I moved to networked backup, I had to switch. Of the two and apart from the network thing, I suppose I actually prefer Chronosync.
As for the firmware problem. If I had this problem, I would … 1/ make a TM backup. Run it a few times to ensure it has everything. 2/ you have a choice of ways to proceed, which you’d have to choose from. E.G, you could live dangerously and trust your TM backup to be ok, so simply reformat your HD by starting up from Restore Disk (boot holding down CMD-R or other (How to reinstall macOS - Apple Support)) then once complete, Restore your User from TM. Alternatively and much less stressful, use a 2nd HD to install Mojave onto, either internally or externally if you have a drive bay or sata cable, then Restore your User from TM onto it. Once finished, you’d then swap out the internal drive for this new one. There’s a few options to achieve the same, but personally, when this stuff happens, I like to have that extra-double-safety-net and would definitely just leave the existing HD alone, until everything was fine with a second one. Either way, TM is your friend here and makes the process much more simple. In the end though, the only way forward will be to either re-format or replace the internal drive and restoring the User from TM is the safest/simplest way to complete the process.
Caveat: I’m not responsible for ensuing catastrophes!
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