Dear All,
Here is the Sollution. Please find the brief SAP reply on this. Thanks for all your helpful answers.
After executing the below given program, all the fields are available in the data source.
SAP has replied on this as below:
Those missing fields from the extract structure are as described in the Note 1810357
1810357 2LIS_17_I3HDR: Fields are missing after upgrade to EHP6
It means that during the upgrade process XPRA did not run successfully, otherwise these fields would not now be missing.
So questions for your upgrade team 
- did they check the log(s) after the upgrade ?
- were the usual upgrade preconditions fulfilled before it started?
In other words, extraction queues must be empty and setup tables must also be empty ... in all clients.
To make all missing fields available in extract structure MC17I30HDR again, report RMCSBWXP_COM must be executed manually.
Because the XPRA run leads to changes in DDIC, the entries for V3 updates, extraction queues & reconstruction tables (setup tables) must either be processed or deleted.
Because you get an error message by uploading the data to BW due to missing fields, a deletion is the only way.
That means, the deltas collected in those queues in the meantime will belost and a complete re-build for all data selected data by DataSource 2LIS_17_I3HDR is required.
So please proceed as follows:
a.) delete the extraction queues via LBWQ (MCEX17 and MCEX17_1) and via tcode RSA7 (DataSource 2LIS_17_I3HDR).
b.) delete all entries from 'Orders' setup tables application 17 via tcode LBWG.
c.) run report RMCSBWXP_COM to add the missing fields to extract structure MC17I30HDR of DataSource 2LIS_17_I3HDR
-> please have a look on Note 640066 for more details.
d.) run report Z_MC17I30HDR_ROOSFIELD_1810357 from Note 1810357 to make the fields visible in the source and in the related BW system.
e.) run tcode OLIIBW to fill the setup tables for orders.
f.) replicate DataSource 2LIS_17_I3HDR from the BW system.
g.) create InfoPackage in BW system to upload data from 2LIS_17_I3HDR.
Please note, that the execution of points a.) to e.) must be executed ina posting free period to ensure consistent data.
These same steps have solved the same issue for another customer.
So please run them by your Basis, Upgrades & BW colleagues.
Best Regards,
Venu Gopal