All of my apps were deleted from my apple id

Somewhere between updating my phone, changing my gamecenter email and password, or transferring pictures from my phone to my computer, my apps were deleted from my apple id. I'm not talking about deleted from my phone, I mean from my apple id. I am 110% sure this is the same apple id that I purchased everything on.

It started with me trying to update 2 apps after getting done transferring pictures last night, and it wouldn't let me. I tried a bunch of solutions and none worked. I downloaded Spotify to my phone no problem, but still couldn't update Clash of Clans and Twitch. Then I went to updates>purchased>my name, and saw my only purchased app was spotify. I was confused because it was still my same apple id, I didn't log into a new one. Then I deleted twitch and clash of clans from my phone and was able to download them. I can use them no problem, but that's not really the problem. The problem is any app that is on my phone won't be able to update when an update comes out, which some of those apps I had purchased with my money.

Two or three days ago I had tried to update my phone from my computer, only to have it go into recovery mode. To make a long story short, the problem was the usb port on my computer, so I changed to another one and it updated fine. I figured that was the end of my problem, but I can't remember if I tried to update any apps since then (other than the 2 last night when I found out this problem).

Last night I changed my gamecenter email and password to the same email and password on my itunes account and icloud account (although I think itunes and icloud are the same thing but I'm not sure). No problems there, everything worked fine. Then later on I hooked my phone up to my computer and itunes told me something about this phone not being used with this computer before (it has definitely been used before). Then it told me to fill in my information, so I put in my address, state, zip. I didn't really think anything of it. After finishing with the pictures, I grabbed my phone and saw two updates (see paragraph 2 for what happened next).

I ended up just going to sleep last night to deal with it today. So today what I did was restored from the backup I did right after updating my phone a couple days ago. That did not fix my problem (I didn't think it would since even on my computer itunes is showing my only apps are the four that I downloaded today/last night (clash of clans, spotify, twitch, and alien blue)). The thing that angers me is when I go on itunes, click on the three dots on top left near music, movies, etc, apps, my apps, it shows all of my purchased apps on my phone. When I right click it tells me who purchased it (99% of them say the same apple id that I am logged into that is only showing the four purchased apps, the other ones are from family sharing). Also when I look at my itunes folder on my computer, it shows all of the apps saved to my computer.

Like I said, for now I can still use the apps, but once an update comes I won't be able to anymore. Sky guide, camera+, night cam, and true skate (and 2 maps on true skate) are what I bought with my money.

So my 2 questions are:

-What caused this to happen/how can I avoid this happening again?

-Am I just supposed to buy those 4 apps again even though I purchased them on this apple id?