When I run transaction ABST2, system gives some amount (unreconciled amount) against some GL accounts.
Please guide me how to find out what is the reason for difference and also how to remove the difference.
I have referred SAP Notes 104567, 124509, 364878 etc. But I did not get any clue as to how to go about removing the difference.
Have a look in the master data from the asset accounting if there was change in the settings. (perhaps you can found postings around that time direct on that account)
Look when you started with SAP if the values where correct. When correct look year by year where you the differences started.
Compare this with a report like S_ALR_87011963 - ... by Asset Number.
When there are differences look if there where posted on that account manual. In the most cases document type is different from AA and AF.
When you have to make a manual correction use the transaction ABF1 (search on this forum how this is working)