In apps the the option to control whether the part should be allowed to Backflush or not is not available yet I think.

If the material is connected to the operation, the system (in apps always assumes the material connected to it has been consumed if you report completed quantity (else how could you have built this quantity?)

Maybe try to not have the material operation connected (but that has other drawbacks).

In later IFS versions you can set the "Reserve/Issue Type" to "Reserve" or "Manual" on the component. This will not allow Backflush even when operation connected unless first reserved. 

For this particular assembly we are assigning several different operations to shop order lines in order to divide the parts into several subassemblies so that all the parts aren’t mixed into one material cart. The material is being picked with a third party scanning tool to issue the components. We are using one shop order to achieve picking and assembly operations.

For example:

If everything is reserved on the shop order, but one part. Their picklist will only show what was reserved. Once they’ve picked all the parts that were reserved they believe their operation is complete so they will approve the operation. IFS will assume it’s all been picked and automatically issue the part that wasn’t reserved or physically picked.

Are we not using routings for their intended use? Should we be using a different function to achieve picking parts into their respective carts?

I know that was a bit vague and out of context. Hopefully you can make some sense of it. Thank you!