Hi Mayank,
I believe anyone who has similar requirement like yours must have faced this issue.
This is because of the reason that the extract structures have controlled architecture with communication structures. Whenever a datasource is activated using LBWE mainly 3 tables are used which controls the fields which need to be visible or not in your extract structure.
Three tables are:
1. TMCEXCFS - This has all the fields in the pool and decide which field should be visible based on status. As shown below, the state is A for MC02M_0ITM but F for MC02M_0SCL.
So it is not visible in the selection of right pane in LBWE for your datasource.
2. TMCEXCFZ - This has all the newly added fields or custom fields added to the extract structure.
3. TMCEXACT - Relation of extract structure with datasource is present in this table.
So ideally when we try to enhance any LBWE datasource it is handled by above tables.
Now what tricky is that you can modify entries in TMCEXCFS to make it appear 
in your communication structure. If you decide to do this you should test it very throughly in Dev system and try to "break the code" (so to speak 
). If your testing is fine then you can change the entreis in table and play with it.
But it is recommended that if you need the additional field you can add it with custom enhancement and not changing the contents of this table.
Please let me know if there are any questions.
Thanks
Amit
PS: please excuse typos.