You're definitely not alone, Wye check valves can make draining return lines tricky because they're designed specifically to prevent backflow, which unfortunately works against you in situations like this. If the valve is installed low and there's no bypass or union nearby, the water will stay trapped unless you can either temporarily remove the valve or disconnect the plumbing upstream of it.
In my case, I had a similar issue when relocating a reef tank setup. I ended up having to cut and later reattach part of the return line because the check valve was glued in without unions. Since then, I’ve made it a point to include unions on both sides of any check valve and even a drain valve on the lowest point of the return line for future maintenance.
If you're planning to redo any part of the plumbing while moving the tank, it might be a good time to rethink the layout for better long-term access. If you’re not comfortable modifying it yourself, a professional can help you set it up more serviceably. I’ve found that getting advice from experienced pros, especially those offering plumbing services Singapore, can really save time and trouble later on.
Let us know how you end up handling it, your solution could help others in the same boat.