Since you’re hosting your ZIP file outside the Ibex Farm, it shouldn’t affect it at all. What will happen however is that, whenever you reach a trial whose resources have not been preloaded yet, PennController will give it another 2 minutes (if I remember correctly) before starting the trial. If the resources are still not preloaded after those two minutes, the trial will start anyway: if you have a wait on an Audio element whose file did not preload, then your trial will never end.
If your design has a multi-part structure, you could consider splitting your resources across as many archive files as you have parts, and insert CheckPreloaded before a part (specifying the corresponding label-s) to only check for its resources.
Jeremy