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I have a number of spectra which all contain the same two Oxygen-III lines. These lines should NOT show changes in the value of the center wavelength and the flux (i.e they should remain constant across all spectra), however some peaks have for some unknown reason, changed dimensionally.

Is there a task I can use where I can select the specific lines/peaks, and then input the values these peaks SHOULD have in order to calibrate the entire spectrum to those values (i.e. shift the wavelengths, rescale flux etc)?

If I understand your question (and data) correctly, I think you're looking for the IDENTIFY family of tasks in the ONEDSPEC package. For example, you could use AUTOIDENTIFY to get the dispersion from a known line list in one of you spectra and then use REIDENTIFY to correct the rest. If this is a simple matter of adding a known offset to each of the spectra then see the SPECSHIFT task as well, likewise SARITH can be used to apply some scale to the flux values via an expression (but note this is not the same as recomputing the flux-calibrated spectrum).