Hi Sagar,
This behaviour is due to note 1705402: to restrict the uploading of the same file more than once.
After applying this note, the report RFEBIT00 will check if you are importing a duplicate file from the bank.
RFEBIT00
.........
select * from FIPYXXD_INSTMT into table lt_instmt where ANWND = '0001'
and BANKS = 'IT' and FILE_ID = ls_instmt-file_id.
describe table lt_instmt lines no_of_entries.
*- initial balance records
ELSEIF UP_RECTYP = '61'. "initial balance records
FEBRIT61 = TAB_EINGABE-TEXT.
CLEAR: UP_AMNT_D, UP_AMNT_C, UP_ANZ.
AUSZUG-BANK+5(5) = FEBRIT61-11.
AUSZUG-KTONR = FEBRIT61-12.
lv_string = AUSZUG-BANK.
lv_string+15(30) = AUSZUG-KTONR.
lv_string+45(5) = FEBRIT61-13.
ls_instmt-ABSND = lv_string.
if no_of_entries gt 0 and flag_ins eq ' '. "Note 1705402
loop at lt_instmt into ls_stmt.
if ls_stmt-stmt_id = ls_instmt-stmt_id and ls_stmt-absnd = ls_
message e885.
endif.
endloop.
endif.
The processing of the files in the report RFEBIT00 is as below:
When the file is uploaded for the first time, then the report creates the multicash files as well as update the table FIPYXXD_INSTMT with the file data. When the same file is uploaded the second time the table FIPYXXD_INSTMT is checked with the details of the file to determine if the file is already processed.
If yes, then the report prevents the file to be processed for the second time. The report RFEBIT00, creates the multicash files, while doing so it generates the statement ID(aznum) from the tabke FEBKEY. It gets the latest statement number from table FEBKEY and adds 1 to it and sends the next statement number in the field AZNUM of the generated files.
Nevertheless, if as in the case you described, you are sure that the files were just generated and deleted by the user without carrying out further actions with the multicash files, you could delete the entry in table FIPYXXD_INSTMT, so that you could run transaction FEBC and get the files generated again.
Hope this information is helpful for you 
Regards,
Carolina