Whether or not you can identify the GOG files (most will have obviously different modification dates or show GOG as their source), the games are unlikely to work without the original installers to write the appropriate registry entries in Win 95. You can probably find those entries in the current Windows registry, then manually edit them into the 95 registry, but that is a giant PITA.

On a side note, Win 95 on a Pi? You can't possibly be running it natively (Win 95 can't recognize the hardware), so it must be some kind of VM. If so, I seriously doubt it has the necessary hardware emulation to give 95 any serious gaming ability.

EDIT - The more I think about this, the more impossible it sounds to me. Removing GOG's compatibility work will also remove a ton of things that replaced the original DRM and certain hardware functionality that many of these games require and will never be provided by the Pi. Basically, the only games I can see this working with easily are the emulated games that run in DOSBox and ScummVM, which don't need 95, you can just run the Pi versions of DOSBox and ScummVM natively on the Pi.