For DSLR autofocus calibration, service usually adjusts the lens, using your camera body as the reference to measure the error. In most cases, that should not make your other lenses worse.

What gets changed depends on the lens design. Calibration may involve a mechanical adjustment, such as a focus position sensor, or an electronic/firmware adjustment, such as internal focus lookup values. Shops use specialized optical test equipment (for example, collimators) to measure focus very precisely; it isn’t generally a practical DIY job.

Sometimes a body can also be checked or adjusted, but if your other lenses already focus acceptably, the likely goal is to bring the problem lens into spec with your body rather than shift the whole system and disrupt everything else.

Before sending gear in, try any available AF fine tune / AF microadjustment. If the lens cannot be corrected within that range, service calibration is the next step. In short: calibration is usually targeted to the misbehaving lens, and other lenses normally continue to work as before.