Hi Juan,
Because the records were deleted when we deleted SMQ1 / RSA7 before the upgrade?
When you have upgrade plan of source system, you just need clear all the queue which holds delta records like SMQ1/SM13/LBWQ/RSA7. need to make them as zero by running respective jobs/delta info packs. The step which you did DELETED was wrong. its delta records, you lost them. Need to find lost delta reocrds with help of source team and reload them with reapir full load(based on proper selections)
Can this missing data be recovered by doing another Initialize with data transfer?
No, with help of source team find newly created or changed records on particular date(ECC upgraded day). if its LO Data sources then delete and fill the setup tables and load to bw side by using Repair full request based on created date or change date selections.
Full repair request: Go to respective info pack, from menu Scheduler--> repair full request. if its disabled then create new info package and choose from above path.
Thanks