There are two issues here, both of which are known problems.
First, the links to the Remote Tools are updated when SP2 is installed so that they point to the wce420 versions. However, 4.0 and 4.1 devices/emulators require earlier versions of the tools. The earlier versions of the tools have the same filenames but are located in the parent directory:
+ Program Files\ + Common Files\ + Microsoft Shared\ + Windows CE Tools\ + Platman\ + bin\ <-- 4.0/4.1 versions here + wce420\ <-- 4.2 versions here
To fix this issue, update or create new shortcuts on the Tools menu via "Tools > Customize... > Tools".
A second problem occurs if you have installed SP2 on top of eVC4 without first installing SP1. In this scenario the tools in "bin" are the versions from Platform Manager 4.0. The SP1 installer upgrades these to 4.1 (which is compatible with 4.0 devices) and but the SP2 installs the 4.2 tools side-by-side (because they are not compatible with 4.0/4.1).
To fix this scenario I recommend that you uninstall SP2 and then install SP1 and SP2 in order.