You can accomplish this task in a few steps:
WARNING: Make a backup of all vdi/vdmk files you wish to compact just incase something goes wrong during the process.
1. Use an android app inside of genymotion such as "Secure Eraser" to Zero fill the free space for the corresponding vdi/vdmk (Use the 0000-0000 option from the drop down list)
Secure Eraser link
https://play.google.com/store/apps/details?id=com.aiuspaktyn.secureeraser&hl=en
2. Shutdown genymotion and clone the vdi/vmdk using the follwong command:
VBoxManage clonehd "file" "newfile"
where file and newfile are the source and destination vdi/vmdk
3. Because step 2 will create a new uuid for the cloned vdi/vdmk you will need to set the old uuid to the cloned copy using the following command
VBoxManage internalcommands sethduuid "FILE" "UUID"
(where file points to the cloned vdi/vdmk and uuid is the uuid you wish to set.)
Thanks for suggestion, such workaround is fina, as long as it makes me able to use that android emulated device for longer time without recreating it from scratch to reclaim used up space :D – chomiak – 2015-09-29T16:47:57.650