Yes. The first instance of this, while not a direct change to the actual base stat values, occurred in Gen 2 with the split of the Special stat from Gen 1. The Special stat was replaced by Special Attack and Special Defence, so Gen 1 Pokemon effectively received brand new base stats. Each Pokemon's old Special stat lives on through its SpA stat or its SpD stat.
Between Gen 5 and Gen 6, a variety of Pokemon experienced direct base stat changes. The list of these Pokemon, according to Serebii, can be found below:
- Butterfree's base Special Attack was increased from 80 to 90.
- Beedrill's base Attack was increased from 80 to 90.
- Pidgeot's base Speed was increased from 91 to 101.
- Pikachu's base Defence and Special Defence was increased from 30 to 40 and 40 to 50 respectively.
- Raichu's base Speed was increased from 100 to 110.
- Nidoqueen's base Attack was increased from 82 to 92.
- Nidoking's base Attack was increased from 92 to 102.
- Clefable's base Special Attack was increased from 85 to 95.
- Wigglytuff's base Special Attack was increased from 75 to 85.
- Vileplume's base Special Attack was increased from 100 to 110.
- Poliwrath's base Attack was increased from 85 to 95.
- Alakazam's base Special Defence was increased from 85 to 95.
- Victreebel's base Special Defence was increased from 60 to 70.
- Golem's base Attack was increased from 110 to 120.
- Ampharos' base Defence was increased from 75 to 85.
- Bellossom's base Defence was increased from 85 to 95.
- Azumarill's base Special Attack was increased from 50 to 60.
- Jumpluff's base Special Defence was increased from 85 to 95.
- Beautifly's base Special Attack was increased from 90 to 100.
- Exploud's base Special Defence was increased from 63 to 73.
- Staraptor's base Special Defence was increased from 50 to 60.
- Roserade's base Defence was increased from 55 to 65.
- Stoutland's base Attack was increased from 100 to 110.
- Unfezant's base Attack was increased from 105 to 115.
- Gigalith's base Special Defence was increased from 70 to 80.
- Seismitoad's base Attack was increased from 85 to 95.
- Leavanny's base Special Defence was increased from 70 to 80.
- Scolipede's base Attack was increased from 90 to 100.
- Krookodile's base Defence was increased from 70 to 80.
Once again, between Gen 6 and Gen 7, base stat changes occurred. They are listed as follows (credit Kaphotics):
- Arbok's base Attack was increased from 85 to 95.
- Dugtrio's base Attack was increased from 80 to 100.
- Farfetch'd's base Attack was increased from 65 to 90.
- Dodrio's base Speed was increased from 100 to 110.
- Electrode's base Speed was increased from 140 to 150.
- Exeggutor's base Special Defence was increased from 65 to 75.
- Noctowl's base Special Attack was increased from 76 to 86.
- Ariados's base Special Defence was increased from 60 to 70.
- Qwilfish's base Defence was increased from 75 to 85.
- Magcargo's base HP and Special Attack was increased from 50 to 60 and 80 to 90 respectively.
- Corsola's base HP, Defence and Special Defence was increased from 55 to 65, 85 to 95 and 85 to 95 respectively.
- Mantine's base HP was increased from 65 to 85.
- Swellow's base Special Attack was increased from 50 to 75.
- Pelipper's base Special Attack was increased from 85 to 95.
- Masquerain's base Special Attack and Speed was increased from 80 to 100 and 60 to 80 respectively.
- Delcatty's base Speed was increased from 70 to 90.
- Volbeat's base Defence and Special Defence was increased from 55 to 75 and 75 to 85 respectively.
- Lunatone's base HP was increased from 70 to 90.
- Solrock's base HP was increased from 70 to 90.
- Chimecho's base HP, Defence and Special Defence was increased from 65 to 75, 70 to 80 and 80 to 90 respectively.
- Woobat's base HP was increased from 55 to 65.
- Crustle's base Attack was increased from 95 to 105.
- Beartic's base Attack was increased from 110 to 130.
- Cryogonal's base HP and Defence was increased from 70 to 80 and 30 to 50 respectively.
- Mega Alakazam's base Special Defence was increased from 95 to 105.
Between Gen 7 and Gen 8, Aegislash's base Defence and Special Defence were both reduced from 150 to 140.