I think the question was answered. Once the medication it out of the system, it no longer has effects on the body.
There are some permanent side effects that could happen such as tardive dyskinesia, though it's not too common.
It is possible the medication does have long term effects that could have developed aside from TD, but the bottom line is if so, there's not too much data on it. Several medications effects are not studied over the course of several years. There is data, for example, that long-term use of antidepressants poses benefits that were not known until a few years ago because this knowledge required that a large number of people be followed for several years after starting it.
People schizophrenia develop a phenomenon known as neuroprotection while on an atypical antipsychotic. In schizophrenia, a person's brain degenerates unless the disorder is treated. Long term use of an atypical antipsychotic preserves the brain. This, however, is only for this with a schizophrenia per studies, though there is reason to believe the same phenomenon is going on in schizoaffective disorder and some other chronic psychotic disorders.
Off on a tangent, one of the benefits I have with working in a forensic psychiatric unit is I have much more liberty to stop patient's meds if I suspect the person is not truly mentally ill with a non-substance use Axis I disorder. So far, I've had 10 patients that were diagnosed with a psychotic disorder or bipolar disorder by several doctors, that when taken off of meds, even for several months did not show any signs or symptoms of the disorders.
Unfortunately, this only strengthened my fear that there are plenty of people out there, misdiagnosed, and the misdiagnosis will only further carry on. When a doctor sees a prior diagnosis, several unfortunately keep that diagnosis without verifying the credibility and validity of the original. Once a patient is diagnosed as psychotic or manic, and put on a medication, then given to a new doctor, it's very difficult for the new doctor to tell what was going before the medication started on unless meticulous notes were taken by the diagnosing doctor.
I just took a guy off of antipsychotics except for Seroquel 25 mg Qdaily that's up for attempted murder. The guy so far shows no signs or symptoms of psychosis despite having a schizoaffective disorder diagnosis (for years), and it's been several weeks he's been on that miniscule dosage. I'm suspecting that the moment I stop his Seroquel, he's going to start feigning symptoms because he doesn't know the dosages where it's supposed to have an antipsychotic benefit. He doesn't know that at 25 mg of that stuff, it doesn't treat psychosis, and given that I've been documenting his coherent behavior for weeks, his attempt to plead not guilty by reason of insanity isn't exactly going to hold much weight.