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I have updated my Sony Z2 from 4.4.4 to 5.0.2 and two "File Commander" are displayed when tap Applications. "Restore to factory" from phone and "Repair my phone" with PC Companion had not any effect. How could I remove the old version?
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This has now been investigated and this is only seen in this specific customization (the software made for your country). The developers are working for a fix that will be included in upcoming updates, but unfortunately I have no info when this will be released.
As workaround you can disable and clear data of the old File Commander and it will disappear, also in the app drawer. Note that, this application will appear again if you perform a factory reset/software repair on your phone.
Thank you very much for your help.
I heard that a new update (from 5.0 to 5.1) will appear in July this year. I wish that the signaled matter to be resolved in the new update for Customization Version 1281-4642_R4C.
How is it better to make the next update? OTA, "PC Companion" using update or "PC Companion" using "Repair my phone"?
I cleaned off the cache data and then disabled File Commander Ver. 3.1.13155 because it no longer update. Now it disappeared from the App drawer.
On phone is active now File Commander Ver. 3.13183 only.
Do you know which of the versions is old, and what is new?
You have disabled the right one. The one that can be disabled is the old version, the new one cannot be disabled, it can only be Uninstalled.
Well, it should not matter if you update via OTA or PC Companion. A software repair via PC Companion is not needed, but if you experience issue and/or strange behaviour after a software update, it's always recommended to perform a clean installation of the latest software via PC Companion.
It can disable any of them.
I do not know who of it will be kept for future updates to keep it activated.
I hope to be disabled the version to be.
That sounds strange. I do not have this customization so I cannot say for sure but you should find one of these applications via Settings > Apps > The tab "Downloaded", this should be the new one. And at the tab "All" you should find the both of them (if both are enabled), so disable the one that is not at the "Downloaded" tab.
Your advice was good. I found the old application Ver. 3.1.13155 and I disabled it.
However, this app remains off on phone and can only be removed in a future update.
Thank you for the info! 
Hello,
I saw with pleasure that the phone was updated.
Now instead of Customization Version 1281-4642_R4C is installed 1281-4642_R5C.
Everything is OK now - the old version of File Commander was deleted completely.
Thank you very much for your support.
Please send my thanks to development team who acted promptly.
With good,
Id2000
Thank you for the updates! I will make sure the concerned developers receives your feedback. 