Looking through D1.6:2007 I don't see any significant changes to procedure qualification requirements from the first edition, 1999. If nothing changed then the procedure you ran pre-2007 is just fine. If the code ever does change its requirements and it wants to allow the use of procedures that do not apply to the current edition but did to previous editions then, yes, it would need language similar to what is found in D1.1. Until that time, the addition of such language could help clarify but it is not necessary to keep your pre-2007 procedures valid to later editions.
That got me thinking. Say I run a PQR with a certain set of parameters and it passed a certain set of criteria I established myself. This is all a test I made up myself. Later AWS publishes a standard with certain procedure qualification requirements. I check my PQR against what this new standard requires. If my PQR complies with all the requirements then I can write a WPS off that PQR stating it is a AWS X code procedure even though the PQR it is based was run before it was ever published. No problems.
The same goes for your D1.6:1999 procedures. There were no changes in 2007 so all is good.