I would be happy to do one of the following:
1. Upload this file and keep it the same for all runs of the workspace (does not work as the "Dynamic path" is different from when the SchemaMapper is run on FME Desktop and it seems this path is hardcoded somewhere)
2. NOT upload the file, but copy the file locally on the server on the same path
'D:\\apps\\FMEServer\\Server\\repository\\xxx\\xxx_schemamapping.csv\\' 2013-04-28 23:53:47| 1.9| 0.0|INFORM|CSV Reader: Done reading CSV files in directory `D:\\apps\\FMEServer\\Server\\repository\\xxx\\xxx_schemamapping.csv\\'
Using FME2012 for the moment, however they are switching to FME2013 in some time. Not sure if it helps anything with this issue?
Also I would say that handing input paths/filenames on FMEDesktop workspaces and then uploading them to FMEServer seems to be quite a challenge.