I'd say the most important thing to do would be to send your manager to a basic HPLC seminar. Sorry for being cynical.
I'd say all important thing's have already been mentioned. Just adding my 2 cents...
As already said, the exact determination of the void volume is far from trivial. There are heaps of articles in the scientific literature about this.
Concerning the "unretained solute approach" one should always be aware of the fact that no matter which test probe you are using (uracil, thiourea, nitrate,...) you are NOT doing a measurement of the void volume. You are determining the retention time of your test probe, nothing less, nothing more. If done correctly, this retention time can give you a pretty good estimation of the void volume. But it's still an estimation, nothing more. Although it should be enough for everyday purposes - for academic/highly scientific research it might be not enough.
How to do it correctly? Obviously you have to use conditions under which your "unretained test probe" actually is unretained. Using 90% aqueous on a C18, as you already found out, definitely is NOT correct. I've got the rule of thumb from somewhere that you should use at least 60% organic in the mobile phase for this and never got problems with this.
And remember (and tell your manager) that the void volume is a property of the column (plus the HPLC system, to be exactly). The mobile phase is NOT involved. Therefore relying on the method's exact mobile phase is nonsense in this case.