Fiora has never been perfect when it comes to how she treats family. She often placed herself in a position of control and protection first, with comfort and emotional bonding second - although not to any level that could be described as stifling. Unfortunately, these tendencies ended up informing her relationship with her son as time went on.
Fiora's straight laced nature could make her something of a difficult mother to have, even if she has mellowed out considerably compared to where she was in canon. She often ended up finding - or deliberately, on some occasions - positioned as the 'bad guy' of the two between herself and Eliwood, something which she would come to regret as time went on. She does still set aside time to bond with her son, most often by taking him out flying with her when they both have the time, but a general lack of shared interests between them also causes further strain.
Unlike what canon says, if Fiora is Roy's mother she's still alive by the start of FE6 - although her relationship with her son has been left strained recently. She's immensely proud of him and the two love each other deeply, but Fiora's controlling and withdrawn nature kept clashing with Roy's burgeoning need to express himself as he grew older. Another part of this is Fiora's own difficult relationship with Hector, tending to view him as something of an undisciplined brute even years later - and always being slightly wary of Lilina as an influence on her son as a result.
The various strains on their relationship eventually result in the two having what would always be called The Argument in years past. The Argument ended with Roy 'winning', leaving to study tactics under Cecilia with Lilina for a substantial amount of time while Fiora found herself fretting over the idea that she'd repeated her old mistakes with Farina once again.
When Roy returns Pherae at the start of the game, Fiora was wounded in the fighting - although not mortally. Eventually she forces herself to face her own fears and concerns, deciding to remain with the ill Eliwood rather than accompanying Roy to meet up with the rest of the League. While she trusts Roy and openly tells him so when they try to make up before he leaves again, she still can't quite resist the urge and does sneak behind his back somewhat to make sure that Marcus, Lance, Alen and Wolt are prepared to look after him should it come to that,