Are you using the DLL object in TestComplete to load the DLL? If so, perhaps the ClearSettingsBeforeEachRun property in the IDLLAccessProcessOptions Object Properties may help.
You could also try experimenting with the process Refresh() and RefreshMappingInfo() methods in the faint hope that they can in some way cause the DLL change to be noticed.
Or you may want try renaming one of your DLLs. Hopefully TestComplete will consider them as two separate DLLs. Searching on "windows rename DLL" brought me to various pages describing the use of DUMPBIN, and finally
https://support.microsoft.com/en-us/kb/131313 "How to Create 32-bit Import Libraries Without .OBJS or Source"