Often times i have trouble swallowing. i am on liquid methadone and often it feels like it was swallowed wrong (pipe) will it still be effective?

It can't go down: "wrong pipe" without causing violent coughing and retching. If you are having swallowing difficulties, this may be related to serious esophageal disease, and you need to talk to the prescribing doctor and/or your primary care physician. It should be evaluated. If it were not being absorbed, you would be experiencing other symptoms.