I am using a refractor with a Field Flattener and even with this configuration I am getting egg shaped stars.
I tried using half of the 550D frame (2600x3465) with cropping values on capture module. Sometimes it works some don't.
Sometimes it defaults to full frame (5202x3465). The solver has the same behavior, but it always defaults to maximum size.
Would it be possible to force a cropped frame on solving? It would be very useful for centering.

The solution of the problem is setting proper distance of your field flattener to CCD. Cropping an image is just workaround.
Check your flattener's back focus in its specs and make sure that you're close enough (i.e. distance from your CCD matrix to the shoulder of your flattener is correct). Otherwise you will always have egg shaped stars and will have to crop every single image.

My flattener is at the correct distance (44mm), but still, it has some egg shapes, that's normal, the field will always have some of them.
Also it's a proper one from the manufacturer and fitted for the telescope model. It has a specific size bayonet adapter to keep the correct
distance to sensor. The ideia was to crop on capture, it also would be faster on download, as it would transfer only "half image".
I think it's a matter of keeping the crop size on the solver image. I was trying to use that workaround, it would be perfect if it was possible to do that.

I use the same flattener. I rarely use my DSLR but when I do I run plate solving on the lowest resolution jpeg instead of full frame raw image. To do so you need to select the mode on INDI panel, not in Ekos. I believe it will let you set image crop as well. Set it up and take just one image with INDI panel. All subsequent images in Ekos would be taken with these settings.

Thanks for the info! I will try that method to see if the solver keeps the cropped size.

Tried that method and it does not work, the solver always resets to full frame size
Will try another aproach, capture frame, frame the object in the left half side, make a reference frame, solve and then crop.