Internal SSD not recognized

I'm hoping you will help me with this issue. It's starting to be annoying. I have a MacBook Pro early 2011, 8.1, and I have made a couple of upgrades.

• First manipulation, I switched from the regular 320 HDD to a Samsung SSD, installed the OS and everything was running fine, 4 years ago maybe.
• Second manipulation, almost a year ago I decided to install the second hard drive, using iFixit Optical bay.

Everything seemed to work until, a couple of months later, I got the folder with the question mark. After a couple of hours of freaking out, I recovered all the data from that disk, and put it in a safe place. So I thought, "my SSD failed", not a big deal, I have another Samsung SSD 850EVO new to put inside. I installed the OS, put it inside, but the computer was not seeing it. Conversely, if the same SSD was used from external mounting, it could be seen and the OS was running perfectly (except for the obvious slowness due to the USB 2.0 bottleneck).

• First Repair: After a quick search on the internet I thought that the problem was the cable connecting the hard disk to the Logic board, so I bought a new one from iFixit, replaced it, and then the SSD was seen from the computer, allowing internal boot.

After a couple of months, the same issue presented itself. So I thought "ok, no big deal, maybe the spare piece was crappy, s**t happens, but I have no money to buy another, so let's wait". I worked with the external SSD until December, 6 or 7 months, when I bought the new cable.

• Second repair, 20 December 2018: replaced the cable, again purchased form iFixit, and also cleaned up the heating paste and replaced it, because the fans were kind of running a lot.

Worked fine until the 21 of February, kind of a lot of stress actually (numerical computations, not difficult but a lot of computation), then I turned it off and went to vacation. Come back yesterday and surprise, no booting.

State of the art: the computer does not sees the SSD drive if it's stocked internally, it sees only the Internal Hard disk mounted on the Optibay. However, I'm writing this post from the same computer, booted from the same SSD externally connected via USB, the OS is running fine. I have run the Extended Hardware check, with the hard disk mounted internally, no problems reported.

I might have fu**ed up the second hard drive installation, maybe I forgot something, but I have no idea on what to check for that.

Can you guys help me fixing this problem once for all? I'm starting to think it is the Logic board that somehow f***s up my cable, still, I'm trusting the Hardware test. I'm open to any detailed suggestion, will provide more informations if you also give me detailed instructions on how to get them.

Thanks to all.