I have figured out the timeline of events prior to the beginning of the story. Please note that only the Sonic material/events I list here are considered canon in the stories history, this should help you figure out what the limitations of the characters ought to be.

The timeline of events goes like this: Sonic the Hedgehog, Sonic CD, Sonic 2, Sonic 3 and Knuckles, Knuckles Chaotix, Sonic OVA (adaptation), Sonic Adventure, Sonic Adventure 2, Sonic Heroes and Shadow the Hedgehog (whichever timeline is the canon one).

For those who are concerned about the contradictory Metal Sonic appearances throughout the timeline, there were multiple Metal Sonics, and robotic duplicates of others as well. If we go chronologically, we have seen:

Metal Sonic mk 1(Sonic CD; Destroyed)

Silver Sonic mk 1 (Sonic 2; Destroyed)

Mecha Sonic mk 1 (Sonic 3 and Knuckles; Destroyed)

Metal Sonic mk 2(Knuckles Chaotix; Destroyed)

Metal Sonic mk 3/Hyper Metal Sonic (Sonic OVA; Destroyed)

Metal Sonic mk 4(Sonic Adventure Easter Egg/ Sonic Heroes; Active)

Metal Shadow(yellow striped duplicate from Shadow the Hedgehog multiplayer; Active)

Mecha Shadow 1 through 4(remaining options from Shadow the Hedgehog multiplayer; Active)

Others that made their debut in the timeline between Shadow the Hedgehog and Heroes Academy (despite making official appearances in other Sonic media, not part of the timeline) include:

Mecha Sonic mk 2(the one with the gold pieces), Mecha Sonic mk 3 (identical to the original, appearance wise, but much more deadly), Metal Knuckles (original debut was Sonic R, but as I said, if it's not in the list, it's not canon), Mecha Knuckles (honestly not sure if it was fan made or from one of the Game Boy games, but I thought it would be nice to include it) and Silver Sonic mk 2 (just to make sure I don't miss any bot).

The robotics listed in the previous paragraph are all active and all active robotic duplicates have lead positions in Eggman's Egg Legion, which will play a substantial role in Heroes Academy Year 2. For now, treat this as a lesson on what's happened and what's out there.

This should help ease any confusion as to what's fair game in terms of the Sonic mythos.