Your question comes down to terminology.
An "upgrade" in IPS terminology involves the conversion of configuration from the lower version to the higher version.
The IPS 6.0(2)E1 upgrade file (the latest 6.0 version you should use) is: IPS-K9-6.0-2-E1.pkg available from this link:
http://www.cisco.com/cgi-bin/tablebuild.pl/ips6
BUT the IPS 6.0(2)E1 upgrade file can NOT upgrade a sensor from 4.1 to 6.0(2)E1.
Instead if you were worried about conversion of your configuration you would have to first upgrade to 5.0(1e). And then from 5.0(1e) you CAN upgrade directly to 6.0(2)E1 using the file I mentioned above.
But by saying that you are not concerned with conversion of your 4.1 configuration, then you open yourself to another alternative that we refer to as "System Re-imaging".
With System Re-imaging everything on the sensor will be wiped out (including configuration) and a fresh manufacturing image will be installed on the sensor.
System Re-imaging can be done to Any version (any version that has a System Image) from Any version.
There are no version requirements because it first erases everything on the sensor.
To do a System Re-image to 6.0(2)E1 you will need to download the 6.0(2)E1 System Image file specifically for the IDSM-2:
WS-SVC-IDSM2-K9-sys-1.1-a-6.0-2-E1.bin.gz
from this link:
http://www.cisco.com/cgi-bin/tablebuild.pl/ips6-cat6500-idsm2-sys
Follow these steps:
http://www.cisco.com/univercd/cc/td/doc/product/iaabu/csids/csids13/cliguide/cliimage.htm#wp1031426