Adjusting timing on one sub amp while measuring both subs played a big role in improving my response prior to running room correction.
Its worth a try.
Also try moving the mic a foot in either direction to see if that drop out changes.
If you adjust phase/delay "before" running room correction then the ARC will just negate those changes. In order for the manual phase/delay changes to be permanent, you will need to do them after ARC is done.