First, I think you should consider what happened to make this occur so you can avoid it in the future.
The only possible way a merge can be offered is, while logged into the account (A) of the group you own, you went to the account page of that account, erased the email address shown, entered the email address for your other account (B), clicked "Change email" and then accepted the merge warning. So, to avoid this in the future, you never ever want to do anything with the email address on your account page unless you really mean it. I must also strongly recommend that you become very very diligent and log out at the end of every session so that you can be certain of which account you are using the next time you log in. I think you did the merge without realizing you were logged into the wrong account.
Now, to correct this and get back to where you were will be pretty tricky but it can be done. You will want to print this because you cannot keep this post open to perform what follows.
Your description made it sound like you merged account (A) of the group you own into account (B) for the other two groups. If that is the case, account (A) of the group you own no longer exists. The group that was owned by account (A) should now be owned by account (B). You need to confirm this before you can move forward. Log into account (B), go to the group you own and see if the "Admin" menu appears on the left side. That will confirm that the group is now owned by the other account (B) and you can move forward.
Since the account (A) you merged no longer exists, you must recreate that account AFTER making certain you have logged out. After you have logged out, there will be a "Sign Up" in the upper left-hand corner of the Groups.io page.
Click "Sign Up" and recreate account (A) using the email address you originally used for that account. Once you have done that, you must find the group you want to "re-own" and apply to be a member. Then, you must log out of Groups.io again and log into the other account (B).
After logging into account (B), find the group you own, go to Admin > Members and accept the membership request from account (A). You then make account (A) a full owner by clicking on the member (account A) in Admin > Members and changing the role from Member to Owner. Once you have done that, log out of Groups.io again.
Log into account (A) and confirm you can access to all Owner areas of your group. If everything is correct AND you are certain account (A) is an owner, you can then choose to remove account (B) or keep it as a backup or whatever you want to do.