I'd definetly change the entire oil charge to OEM recommended oil. Also change the oil filter. The OEM's have their reasons for specific oil. There is a chance that the oil uses different additives that could prove detremental (i.e. gumming up etc.) Too expensive a piece of equip. to take a chance.
Go to McQuay.com, (public site) and you can probably download the literature for that unit,look for a revised OM\IM. They also have some free design tools there if they are still available. Psych tool,Pipesizing tool and duct sizing tool.
go with what the chiller calls for. i would change it, run it for a short while and change it again. the oil it uses is not cheap and the oil filter is real expensive. i would not change the filter until you get the wrong oil out. if a contractor put the wrong oil in i would let them pay for it.
Eal 46 oil is for R-134A refrigerant so I am assuming that your machine has 134a in it since you did not state so, change the oil and run for 24 hours and then change again. take an oil sample and have it tested and let it dictate if ok since McQuay oil or any factory oil is so expensive!!!! if you have R-12 refrigerant then use 4GS oil and do the same proceure.