idoc to file scenario; multiple idoc to single file and Records missing

Hi All

I require inputs urgenlty and appreciate help.

Multiple idoc to single file scenario; Bundling is used in R3 end, hence idocs in bundle arrives and single file is generated using the below setup.

2 ICO created,

a) first ICO appends all file

b)second ICO adds timstamp using java map

Observation:

1.during the run, idocs bundle size is same till ico's append channel, but after append has happend the final ICO creats file which is smaller .Example 8MB bundles arrived in PI and processed file was 3MB

2.Also duplicate records were also observed.

Please suggest,

Thanks