everything is good except missing you
When my boyfriend ask me how was your day, I answer "everything is good except missing you" is there any problem with my response?

Question

Answer

"everything is good except missing you"

It depends on what you're trying to say. 
If you want to say that your boyfriend's presence has been missing from the environment,, then you can say it like that. 
But if you want to say that YOU are missing HIM, then it would be better to say "Everything is good, except I've been missing you."

If I was your boyfriend, I'd prefer the latter. :-)

Answer

Everything is good except for missing you.

Answer

Everything is good except that I miss you :)

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