Hi Katherine,
Your procedure should not have changed at all. The only change we added is the ability to park the EFT run while you were waiting to find out if it went through correctly.
1. If Telpay is asking if you want to delete the batch (in Telpay) then you would want to say yes, because you will want to submit a corrected batch. From your description you're submitting the entire batch from Telpay. Adagio doesn't ask you if you want to delete a batch in a system check run. Saying no just means you want to reprocess that check run.
2. Nothing should have changed in your process here. If a vendor is not included you need to look at the vendor's transactions to find out why.
Are you using approval? In the company Profile > Batch/System Check tab > Require Check Run approval - if this box is checked you will have an approval button you must click before the system check run can be posted and the EFTs sent.
3. The Technical Support forum is probably the best source of information.