I don't remember you working with me in Moscow.
In this case you can only use:
Я не помню, чтобы ты работал со мной в Москве.
or
Я не помню, что ты работал со мной в Москве.
Former means more negative attitude (statement that you did not work with me). The later means just that I do not remember.
This can be better illustrated if we omit the negative particle.
Я помню тебя работающего со мной в Москве. = I remember you when you were working in Moscow. I remember the expression on your
face and how you were looking then and how you looked and behaved overall and how you dressed, and what were you habits, your character and overall what a man you were at the time. Note, this implyes that you became different since then! Example: Я помню тебя работающего со мной в Москве, ты тогда был очень весёлым и одевался очень стильно.
Я помню тебя работающим со мной в Москве. = I remember the exact moment when you were working, when performing a task, doing a job exactly in the process. Example: Я помню тебя только работающим. Ты вообще когда-нибудь отдыхал, когда был в Москве?
Я помню, что ты работал со мной в Москве. = I remember the fact that you worked with me in Moscow, and nothing more.
Я помню, как ты работал со мной в Москве. = I remember you working
with me in Moscow (I remember you day-by-day and common tasks we
were doing and what we accomplished together)
So you can see that if you say "Я не помню тебя работающего со мной в Москве." the meaning would different from what you intend. It would mean "I do not remember what a person you were when you were working with me in Moscow, your face, your mood etc."
Ты говоришь, что ты тогда был очень веселым. Возможно, но я не помню
тебя работающего в Москве. = You said you were very joyful at the time. Maybe, but I do not remember you when you were working with me in Moscow.
Maybe I remember the fact, but no your look in the process. For instance you can say:
Я помню, что ты работал со мной в Москве, но тебя работающего не
помню. = I remember that you worked with me in Moscow, but I haven't meet you at workplace.
Compare:
Я помню, что ты работал со мной в Москве, но тебя работающим не
помню. = I remember that you worked with me in Moscow, maybe I saw you at workplace, but I haven't seen you working, performing the tasks (rather than talking, joking, entertaining yourself).
By the way, if you add a comma you come to a completely different meaning:
Я не помню тебя, работающего со мной в Москве = I do not remember you, who is working with me in Moscow.