1)If you don't obey me, by the time I get back you may have gotten into some problems. (🤔 Probably is all right but.....)
2)If you don't obey me, by the time I get back you may get into some problems. (This one feels better)
Can two of these be used?
Thanks for not leaving me alone in this one🙂

Question

Answer

Personally, I find “ obey”rather an old-fashioned word to be honest.

I would prefer to say” if you haven’t done  what I have told you to do , by the time I get back, you will be in trouble.

I hope that helps.

🙏

Answer

Obey is normal; however, if someone says "Obey me" it comes off to other people as a person who is self centered or controlling. 
Obey is normally used to refer to rules, like, "please obey the rules." Probably what is more commonly used is "follow the rules."

Answer

It depends on the context and who you are talking to.  One way of saying it could be:
If you haven't done as I told you, by the time I get back, you will be in trouble.

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