Taken from Wild Mass Guessing of Phineas and Ferb from TV Tropes.
My theory of how it could be possible:
After the break up Doof and Charlene got married and had Vanessa but they divorced after her birth but before Candace’s. Doof still shows that he has feelings for Linda (and vice-versa) and they marry and have Candace. When Phineas was born Doof probably built a baby carriageinator for Phineas, but he failed to do so and the machine probably blew up (or went berserk) and seemingly killed Doofenshmirtz (But it didn’t). He was buried after the “funeral” but luckily he had his Dig up a Graveinator and dug it up. People don’t remember that Doofenshmirtz was ever killed and believed he never did. Charlene still realizes he’s still around so they both do the custody agreements on Vanessa. To this date, Doof never revealed any of this to this date, not even to Perry. And to make things stranger, Everyone in the Flynn-Fletcher family has seen Doofenshmirtz in the present day EXCEPT Linda. Coincidence? I say NAY! Even though he and Candace talked face to face, they probably don’t remember each other because it’s been too long or Doof pretended to not know her.
Stated in “Make Play”, Candace is still 15 meaning that her and Vanessa are at leased a year apart since their birthdays are in summer (June for Vanessa and July for Candace as proven in D.W.G.T.B.B.T and C.L.H.H).
More evidence you say? Check it. Both the Flynn kids have at leased 1 trait Similar to Doof and Linda:
Phineas: Obliviousness from his mom. The ability to build stuff in a short amount of time (Like Doofensmirtz). Ferb probably gets it from his own mom but I don’t want to go into that…..yet.
Candace: Craziness from her mom. Being able to survive things that normally kill a human (Just like Doofensmirtz). Also if you notice, they are BOTH are very bad at planning which is why they usually tend to fail at their schemes.