Question

Is it possible to keep the original e-signature when exporting the source PDF file?

Answer

The input images/files are pre-processed by FlexiCapture or 'dis-assembled' on input and then those files are 'assembled' back on the export. So, they are modified in any way. That's why the e-signature is lost as a result. As a recommendation you could try to store the original input files separately before they are entered into FlexiCapture processing.