You can pretty much do anything to your tools within reason. Your tools are typically made from metal and to apply changes would most probably be in the form of machining or welding and machining.
When your designer initially designs the parts he should have been thinking in the back of his mind what areas are of concern and what areas may likely need to be changed to reduce problems like wearing of the tool or potential stress areas that may cause the parts to break by the consumer.
When your designer supplies you with drawings he should include a 2D drawing highlighting and listing possible areas of concerns and he should design the part in a way to make it easier for change.
Say your designer made a hole in your part that was 15mm diameter. If further down the line you decide that 15mm diameter is too small and you want the hole bigger. Dependant on the method your manufacturer made the tool it could be an easy change or a drastic change costing you dearly.
When your manufacturer was first given the 2D drawings they should have taken note that the hole diameter needs to be a development area and therefore he should have designed the tool accordingly for minimal costs.
You will more than likely be paying more for your tools but it would be worthwhile if you are unsure of certain factors. Making the tool as versatile as possible will save money and time.