Full ETL Load into PRD working around system downtime

The problem we have got is some of the Informatica ETL tasks will run 30+ hours on Prod. But, we got overnight backups and batches, which means we got only 18 hours max per day and we got to stop ETL at this point. When we stop the ETL, it sends a truncate signal and wipes all the data out.
Is there a way to make a task not send the truncate signal, instead commit to that execution point and start from there if the ETL is stopped and started due to overnight activities on the production system? Or is there a way to say this task will run at this particular time, so that we can cancel the overnight backups?
Thanks in advance for any help you can offer

Hi,
The tables which get truncated or a rollback occurs in both in SDE's and SIL's. Its only particular tables which get rolled back, not the entire warehouse. This happens in particular SDE's and SIL's, as some of the tasks take quiet a while to complete. Yes, we have gone through Oracle performance recommendations and applied most of them which could be done within the timeframe we have got.
For ex, say Payroll data is being loaded, which might take 25+ hours, we got a daily window of 17 hours. At this point, when I stop the ETL, it marks the task as failed, either SDE or SIL. What we want to do at this point is, for the staging/target table to commit itself instead of doing a rollback. This will enable the task to pick up from this point rather than running all over again.
I had tried changing the commit settings to 5000 rows instead of 10,000 rows by default, in Workflow manager. Also, I enabled persistent cache for these mappings, and changed the 'recovery strategy' to 'restart from previous commit point', both seemed to have made no difference.
Thanks.

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