Hello,
@valerio.manenti
just as a hint, Reconfiguration is not part of TM415. You do not find any note about ProcessParam or ProcessConfig. So for the others TM416, 417. 
@Michal_Malek
The Mapp-Configuration Files can be seen as Files on the CF-Card. So it is typicaly irrelevant how much of them you create. They just lay around, BUT:
There are Mapp-Functionalitys searching for some of this files, and these Files will be startet to interpret and actuate the Systemfunctions.
For a Axis this is the .axis File.
The System goes over each File and analyses the content.
If the Axis is not Referenced to an other Hardware-Axis Component (Acp,PureVAx,…) this message will appear in logger.
-2141192186 The Component “gAxis1” of type axis was found in the configuration but it has not been created.

You can access it in the Cockpit too, with same Information and Empty Pages.
For a PureVAx this is the .purevaxcfg File
The System goes over each File an analyses the content.
If like in this case there is no valid axis Reference, there is a logger entry and operation for this object will be shut down.
-1067448313 Value of Axis Reference in the settings is invalid.

For a LimitSet this is the .limitset File
Here it is a bit different, these Files are gathered to a limit Set List in Memory.
A sum of the contend of all these Files.
They are only used if they occure in any other element as Reference.
Limit Sets can be used via some Commands from Axes Group thats why they are hold ready even if they are not referenced.
The green Part of Configuration Files which are Referenced to each other and combined lead to a working Configuration , does not have issues with the red part of laying arround pre Prepared Files which are not Referenced.
In gerneral i would give the Advice to think about the ease of use which files you pre Prepare in AS and which Configurations you will better Reconfigure with ProcessConfig/Param during Runtime.
Usecase CNC-Machine with different Mechanics
Variant 1: XY
Variant 2: XYZ
Variant 3: XYZA
Prepare a .mechanicalsystem for each system, we can use them in the AxesGroup as Reference. So you don’t need to use ProcessConfig here…

Prepare all .axis for all Axes we can use them in the Hardware as Reference. So you don’t need to use ProcessConfig here…

For the AxesGroup itself i would only use one Configuration File, as there is only one AxesGroup. You cant prepare more of them in advance the system would just try to activate an AxesGroupInstance for each configuration File.
Here it is better to have one ConfigurationFile with minumum Inital Settings (XY)
And then use ProcessConfig to reconfigure this Configuration.
The same would apply to the PureVirtual Axis or Acopos.
Just have one for each Object you will finaly have in your machine, and then set up the nessesary Parameters via ProcessConfig.
If you want to have a Axis in some cases as ACOPOS, and in other cases as Stepper or as a VirtualAxis you have to be sure to not have the reverence active on more than one axis. Be sure you remove the Reference to the logical Axis-Object on the not active ones!
You can use “SYS_Lib - SYSreset()” to execute the required Warmrestart via Software.
ProcessParam can change less Settings, but does this without the need of a Warmrestart. But it is not Retained.
After this general descriptions, to your inital question:
If there is only one Virtual Axis you have intended to generate, i would only use one .purevaxcfg Configuration Element and not 3 of them.
Same for the .axis object.
There are possibilities were you can combine several pre Prepared Files, but its just to confusing.
Better make a Task with ProcessConfig, which you will any way need to adapt References. Just handle all Parameters there. You can Program a nice CASE routine were you select a Action which contains your Parameter set.
For Limit Sets you can use as much pre prepared Configurations as you want.
They can be Referenced to the used Axis.
The error you descriped with the PowerOn was not seen in my Tests, we have to go more in detail if this keeps happening. As File upload is limited, i would suggest to uplad just the mappMotion Config as .Zip. so we can import it in a Project. I assume you do not have jet something special in Hardware- or Logical-View. PureVAxCfg_1 is normaly not influenced by PureVAxCfg_2 it is not of interesst if the 2ten one has no AxisReference in it.
Greetings
Michael Bertsch