I see you created a normal support request, the problem of which is closely related to this issue. If you have a question about an Echelon product then then you should log a support case rather than using the community.
If you deleted anything such as the /Lonworks/types you can easily replace them. If you purchased the smart server then you should be in possession of an installation CD for at least smart server version 4.04.119. Firmware files. This installation CD can be used to install a default fresh version of the firmware files onto your PC and then you can FTP the required files to the smart server. Note that the current firmware version that supports the CPD3000 V2 is contained in a Smart server Service Pack that is available from the echelon web site at http://www.echelon.com/software-downloads?ele=153-0590-01A. Installing this service pack will provide an updated types and import folder that support the CPD300V2 as well as other improvements.