Using multiple workspace environments ArcGIS Python

You can have only one 'current' or 'active' workspace. The ListFeatureClasses() function is similar to 'dir' command in windows command line - you can list only one 'current' dir at time and if you need more, you need to switch.

Use for cycle to iterate over workspaces:

import os
import arcpy

# Set environment settings
workspaces = [
    "C:/eis/eis shape/UPDM.gdb/P_PipeSystem",
    "C:/eis/eis shape/UPDM.gdb/OtherCompanies",
    "C:/eis/eis shape/UPDM.gdb/NEO"
]

arcpy.env.overwriteOutput = True

# Set local variables
outWorkspace = "C:/data"

try:
    for ws in workspaces:
        arcpy.env.workspace = ws
        # Use ListFeatureClasses to generate a list of inputs
        for infc in arcpy.ListFeatureClasses():

            # Determine if the input has a defined coordinate system, can't project              it if it does not
            dsc = arcpy.Describe(infc)

            if dsc.spatialReference.Name == "Unknown":
                print ('skipped this fc due to undefined coordinate system: ' + infc)
            else:
                # Determine the new output feature class path and name
                outfc = os.path.join(outWorkspace, infc)

                # Set output coordinate system
                outCS = arcpy.SpatialReference('WGS 1984')

                # run project tool
                arcpy.Project_management(infc, outfc, outCS)

                # check messages
                print(arcpy.GetMessages())

except arcpy.ExecuteError:
print(arcpy.GetMessages(2))

except Exception as ex:
print(ex.args[0])