I'm aware it's been a couple months, but this problem is getting infuriating for me.
I work with stock images, which of course need to be resized and combined. Force pixel alignment is always on. Move by whole pixels is always off. I always ensure there's no decimal points in any Transform fields.
Often, however, I will have an issue like this: I will take a stock image, work with it awhile, and resize it. There's still no decimal points to be seen, or sometimes if there is, I will alter it to remove them. Then, attempting to merge this initial layer (either as the same file, or a new one) with any Adjustment layers blurs the entire image. Multiple merges (or exports, for that matter--as .PDF even, which to my understanding should NOT anti-alias this way?) blur it further. Even creating a blank layer and merging it down with the existing one, or merging the existing with the blank, blurs it badly.
Anti-aliasing aside, what irks me is that the preview space is perfectly clear until this merge or export. I think a what-you-see-is-what-you-get approach is extremely important. I shouldn't have to guess whether my export will have full clarity or be blurred. The program should be working with me to create what I want; I shouldn't have to fight with it and struggle to predict what it might do.
One thing I noticed is that if I pay -very- careful attention to which direction the blur is occuring (shifting left or right 1 whole pixel, for example), I can move the layer -in advance- 1 pixel in that direction, and then the blur on merge will not occur. This suggests to me that the anti-aliasing is taking into account pixel position that isn't actually accurately reflected in the Transform fields at all, but my understanding of it's all too basic to be certain.
I really hope that we get a fix for this (and for the completely unusable Color Replace tool, but that's a whole other story), as I really like Affinity and would love to see it succeed. Such serious issues in such basic functionality are hard to work past, though.