Well, one possible solution would be that a 10-run manufacture would be actually 10 distinct runs queued one after the other. Resources would be taken for every run individually, initial time and money costs are only an estimate.
Pausing = print completes the current run, but won’t start the next one. Nothing gets wasted.
(perhaps adding some player defined cost/time threshold at which the print pauses automatically)
Cancelling = print abruptly cancels even the current run, materials are wasted.
Delivering manufacturing stuff would take whatever was completed up to that point.
Risk regarding supercapitals and such (as mentioned by @ISD_Fractal) remains. So, it wouldn’t do much for the OP’s problem, though it might give at least levels 1-9 of research finished - just 10 would be scrapped, no matter if it was just started or is nearly completed. Better than nothing
Risk of many runs of a small job (say ammo) would be completely eliminated - but I don’t see this as a bad thing.
Furthermore, this opens another possibility - make a long many-run manufacture while you do not yet have all the materials. Which opens a possibility to add another skill that increases max manufacturing/research time (perhaps 2 skills, one for each). Say current 30 days base gets decreased to say 10 days, then each level doubles the max time and the 5 gives infinite time. As you don’t require all minerals at start, you would be able to set and forget the job, checking on it only to deliver what was completed as the stock on the market runs out.