From my understanding, operon is a series of genes that are regulated by a single promotor. In many cases genes in an operon form subunits of a protein.
Genes in an operon can code for protein subunits, but they can also code for separate proteins. Often an operon will have a few genes responsible for one core function, with other accessory genes that may help regulate or enhance that function is some way. Sometime genes are fused, combining multiple subunits into a single gene. In other cases, subunits can have related functions in the absence of other units.
For example, The ArsAB complex uses ATP to pump arsenic from bacterial cells, conferring resistance. But many bacterial Ars operons lack the arsA gene. Minus this subunit, the ArsB transporter still functions to efflux arsenic from the cell, just less efficiently, harnessing the proton motive force instead of burning ATP.
... ended up finding that one of the genes in an operon was missing.
Does that imply the protein made from those genes in the operon will not be made properly or other genes will compensate for the loss?
If the gene is truly missing, it's can't be transcribed, and the subsequent protein can't be made, but the remaining genes will probably still work. I would start by asking what the operon's function is, and then consider whether the missing gene is essential for that function (hint: If it's missing and the rest of the operon is still there, it's probably not essential). If it is essential, then consider whether it's truly missing. Are there other open reading frames in the operon that could encode something with similar function? Could the organism have multiple copies of the same operon (possibly found on a plasmid)?