I have a NAS from Synology connected to the Giga Connenct router at home. If I now connect the RT2600ac in between as a WLAN router and switch the bridge mode on the Connectbox in between, can I then also configure the WOL remotely? with the Fritzbox this is supposed to be possible.

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You could then activate the VPN on the RT2600ac router to access your NAS via VPN. 
It's certainly not the most secure connection, but at least it's not directly on the network without VPN.

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Question about Synology RT2600ac

I have a NAS from Synology connected to the Giga Connenct router at home. If I now connect the RT2600ac in between as a WLAN router and switch the bridge mode on the Connectbox in between, can I then also configure the WOL remotely? with the Fritzbox this is supposed to be possible.