I loaded my save and suddenly my boxing gloves were gone. I also don't see Floyd in the bottom of Desperado but the door is open, and my trunk of my car is missing.

Any ideas? Can I edit my save game to fix or am I fucked? If so, that's a huge bummer as I basically have to start over.

Not sure about floyd and the trunk, but for the bonxing gloves you can give them yourself with a save editor

Also do you use the unofficial patch ? You should use it to avoid bugs

I'm using just the base GOG install but I thought it includes all of the patches, does it not?

I know what's the deal with the trunk.

It is a known issue, the bug of the Too Many Items.
If you have too many items, AND you try to access your trunk in a place where your car is not suppopsed to be, you get all kinds of bugs and crashes. Same with trying to use the car from a place it is not supposed to be.
Also, the trunk might just disappear randomly even at the proper place if you have Too Many Items. This can get fixed to re-enter the map, or drive to a different location.

The EVEN BIGGER problem is, the Too Many Items bug is only stable in the release-version, and not in the patched version, meaning if you don't try to access the trunk/car at an invalid position, there won't be any other consequences (bugs).
Under the patch, the whole thing causes all kinds of extra problems, which you can't get rid of.

So the only known solution with the GoG-version is to rely on spare saves, and watching your party and car to never get overpacked (I don't remember the moment if the trunk has any weight-limit or not though, and if not, be extra cautious).

This is a reason why I want all patches to be optional...

Someone corrects me if I'm wrong, but no the GOG install only includes the latest official patch, not the unofficial patch

They did it for Vampire bloodlines (pure bug fix )

Was that something GOG patched that you couldn't opt-out of?

I would ask for a refund.

I don't know I don't have the game, but I think there is a version without the patch also
Why are you against unofficial patches ? When they are only bug-fix I don't see any problem

Heh... But in fact they do. Currently selling distribution containes at least HiRes patch by Mash. And it is 100% fan-made. I'm not sure about Killap's unofficial patch in the late re-release. Won't buy a game for the sixth time just to check. ))) Interplay surely had it partially included along with SFall. Unfortunately, usually they are not. I've been involved in the modding group with rather puristic approach. And you know what? Majority of the communty requested 'reacher experience', fixing of the exploits etc. And as a result a puristic patches were requested mostly by the very very minor number of fans. And by publshers, LOL. While most of the communty prefered not so strict alternate mod-o-patch with ambigous solutions.

I guess between "puristic" patches like you say, and patches taking a lot of liberties, there is a "middle", patches who will take take a bit of liberty but will restrict to the original idea of the developer

You usually can't know that idea exactly. That idea can be controversial towards the finally released product. That idea could deserve to be rejected during development (like Burrows in Fallout 1 for example). You can have a fair numbers of the possible resolutions for an exploit or logical error or underdevelopment. You can be 100% sure only on the obvious technical bugs and obvious unfinished content which has enough resources left.
NMA for example, has a simple rules: made by the developers -- patch, made by the communty -- mod. It's that simple