I have honestly never seen a technology deal with royalties done between 2 companies prior to the issuance of an actual Utility Patent. I'm not saying it isn't possible, but I have never seen it.
Since a patent cannot be enforced before it actually issues (if it issues), paying royalties until then is unnecessary and likely a waste of money.
If after a patent is published (at 18 months after filing), someone copies it, and one can prove the infringer was aware i.e had seen the patent, one could potentially sue for additional royalties from that point until the patent issued.
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