Hi Chris
I suspect the warning came with pre wired ESCs, where changing the connectors can sometimes invalidate the Guarantee.
If your brushless connectors are the wrong size or type you may have no option but the cut off and fit the correct ones, unless you can change the connectors on the ESC. if you don't want to alter either then you could make a very short conversion lead with the relevant connectors at each end.The length should be kept as short as possible to avoid the chance of introducing any timing issues.
Replacing connectors should not cause any problem if you cut and replace very close to the original connectors.

Hi Chris, there is no problem replacing the connectors. Just buy top quality, possibly gold plated type for good contact.
Make sure that they are soldered and heat shrinked insulation applied. DONOT crimp the leads this can cause resistance in the connector. Lipo's will produce a lot of power so melt downs do occur.
There is quite a discussion on the forum about soldering connectors, have a read and order the right size, either replace both ESC and motor with matched or match to the larger size, (bigger contact area)
Regards
Mark