Were they assimilated? Displaced? Were they in favour of the mainland Chinese populating their island?
EDIT: The question was about indigenous Taiwanese (Formosans) so my answer is not very relevant, but I'll leave this comment up anyway.
While the Taiwanese people were citizens of the Japanese empire prior to 1945, they were never considered fully Japanese, and they were always reminded that they were Taiwanese. Something similar happened when the ROC occupied Taiwan in 1945, the locals were considered second-class citizens.
The newly arrived ROC officials didn't do an amazing job administering Taiwan and there were soon anti-government uprisings by the locals who were unhappy with their new rulers. In 1947, 228 Massacre occurred, and started a 40-year period of martial law called White Terror under which many local Taiwanese were persecuted. It was a critical event that strengthened Taiwanese identity.
ROC immigrants never made up more than 15% of the total population of Taiwan. The ROC propaganda and educational system brought the Chinese identity to Taiwan. The kids were taught they were Chinese and this did make many Taiwanese people start to accept the Chinese identity, but this only succeeded to a limited extent and Taiwanese identity was always present.
With the liberalisation and democratisation from the late 1980s, people were free to choose their identity without having to fear for their lives. The ROC immigrants, who were allowed to travel to the PRC, realised that the China of their youth doesn't exist anymore. Descendants of the ROC immigrants were starting to feel a stronger connection to the land that they were born in and grew up in, rather than their parents' homeland.
In 2022, most of the ROC immigrants are dead and their descendants mainly consider themselves Taiwanese. Combined with a strong native Taiwanese identity which predated the ROC, Taiwanese identity is very much alive and kicking.