Hi Raghunath,
This part of your requirement "Our current functionality in BI XI 3.1 is we have Macro code that refreshes a report saves the whole report to a xls or pdf file" can be achieved with Report Engine java SDKs in BI 4.x versions, However the sectioning part is not possible as those features have been deprecated from the Report Engine Java SDKs.
Please refer to the samples available at below link for refreshing and saving a report as pdf/excel through Report Engine java sdks.
http://www.sdn.sap.com/irj/boc/index?rid=/webcontent/uuid/30e2b6d2-2784-2b10-59b6-95b2d8c50a02
The options you are looking for can only be achieved from REST SDKs for webi in 4.x versions. Reason being SAP has removed most of the features from the Report Engine java SDKs in BI 4.x versions and are focussing on developing towards REST SDKs for webi.
And it is best to move forward to REST as it is the future roadmap SDKs as far as SAP is concerned.
Hope I am clear in my explanation.
Thanks,
Prithvi