@Jorn-H 

You should replace Ethernet cable connecting Main Deco to TP-link ER605.

Also, TP-link ER605 is Omada, does it not have Web page that reports its Ethernet ports negotiated speed? Check what does it say there. 

Hello Alexander,

I have allready tried a few cables, I have switched one right now to test again. When looking into the web interface I can see that the ER605 sets the port that the deco is connected to to 100m, even if I manually set it to 1000m it will still stay on 100m. I will order another new cable cat7 or something like that to see if that helps.

  @Jorn-H 

This is how I understand your problem description: after restart, Main Deco runs at full speed, then after some time link speed gets downgraded to 100Mbps.

You ask if there is a setting that you may need to change in ER605 to avoid that. There can't be a setting which says "run link at gigabit speed and if everything is allright drop that speed to 100Mbps, just because."

That leaves three obvious suspects: ER605 Ethernet port, Main Deco Ethernet port and Ethernet cable linking them both.

Ethernet cable is the most common cause.

You can (and should) try different ports on ER605 and Main Deco if you haven't done it yet. You can promote Satellite X50 to Main Deco to swap them, for uncommon case of all three Main Deco Ethernet ports having issues: Changing the Main Unit for your Mesh Network

With Ethernet cables, newest is not always better. In last few years amount of counterfeight Ethernet cables, or saying differently, cables not up to claimed specs, has increased substantially. 

Get new cable from different vendor and if possible, from different marketplace. If you have discounter electronics store nearby, visit it and see if they have Cat 5E cables. The ones that look like they've been on the shelf for many years are those you should choose from. Cat 5E is perfectly capable of delivering gigabit speeds, consistently.