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After searching some more, it seems that the following thread may be related to my issue :
After following some steps by the other poster in the thread mentionned, I managed to work around the path problem. However, it seems that I may now have an environment problem :
[INDENT]Unable to complete operation.
Error executing tool.: ERROR 000229: Cannot open C:\arcgisserver\directories\arcgisjobs\pathToService\je21b3d49f57f48609764fb57a445bc02\scratch\scratch.gdb\FEATURECLASS Failed to execute (Make Source Feature Layer). Failed to execute (SearchByFeaturesID). Failed to execute (Search By Features ID).[/INDENT]
Indeed, on the server, I cannot find any path named C:\arcgisserver\directories\arcgisjobs\pathToService\je21b3d49f57f48609764fb57a445bc02\scratch\scratch.gdb\FEATURECLASS. My instinct tells me it has something to do with the environments but I have no clue how to fix it.
Help is still needed, thanks!