Created a new gnome character. Gnomes gain the CRB racial trait of Gnome Magic, which gives them innate spells of Dancing Lights, Ghost Sound, Prestidigitation, and Speak With Animals.
In the APG, gnomes can take the alternate racial trait Magical Linguist, which replaces Gnome Magic and Illusion Resistance (which works as expected).
However, the character sheet now displays the Gnome Magic racial trait innate spells (listed above), and the newly gained spells of Arcane Mark, Comprehend Languages, Message, and Read Magic. Then, if I change the character's race to Dwarf (or something else not gnome), I still have all 8 of the innate spells available.
So, racial innate spells are not being reset upon removal of any trait which contains them.
Quite likely related to - Domain Spells not removed when domain removed
All fixed now -thanks for the report.
I don't know if you have to go through each race or not. But it also affects Kitsune Magic.
This issue was resolved and closed almost a year ago. I suspect your issue might not be exactly the same. Please open a fresh data bug and describe what you are seeing. I'm betting this is more likely a matter of the spells aren't actually being removed then this issue where the spells were actually persisting.