A game's save data is data that re-appears after the game is powered off and back on again, such as SRAM data (also known as "cartridge RAM") on a Game Boy cartridge. The entire save data is referred to as a save file (it is officially called this in Generation II), and emulators may create a save file to store on something such as a computer's hard drive.
Usually, if the save file is deleted, all of the player's progress on the game will be lost. This can occasionally happen with glitches, though not as often as some people may believe (for example, glitch Pokémon cannot erase a save file unless a Super Glitch move is viewed with bad cached screen data, which would have a chance of corrupting the save file). A save file can also occasionally be wiped while using codes from a cheating device.
When a save file has been damaged in a certain way, the game may claim that "The file data is destroyed!" (Generation I handheld games) or "The save file is corrupted!" (Generation II handheld games).
In these cases, in Generation I, the message appears before the New Game/Option screen and the Continue option does not appear. In Generation II, the Continue option may still be present, but selecting it causes the previously mentioned message to appear, and the game will refuse to load it.
Alternatively, when a save file has been damaged a message informing the player about it may not even appear, and the Continue option will be removed. This can happen in Generation I after saving the game when there is no hex:50 terminator on the player's 11th name character or less. This is possible through the ZZAZZ glitch when the hex:50 characters are not at a 'multiple of 3' letter (i.e. 3rd, 6th, 9th and 11th characters).
Internal battery problem
Save file corruption or deletion will eventually happen in a Generation II handheld Pokémon game. The internal battery is used up for the internal clock data as well as progress save data, and the internal clock keeps running even when the game is powered off. This drains on the battery.
Pokémon games from Generation III and onward such as Pokémon Diamond and Pearl save a backup save file; so if the player's current save file has been corrupted the game will try to load the last valid game save.
In the Generation III games, the player's main save data is stored in flash memory rather than a battery, with the battery being present only in Pokémon Ruby, Sapphire and Pokémon Emerald due to Pokémon FireRed and LeafGreen not using the internal clock.
Because of that, you cannot evolve a Eevee into Espeon or Umbreon in the Kanto remakes.
If the battery is fully drained, the game will display the message "The internal battery has run dry. The game can be played, however, time based events will no longer occur." in the third generation games.
Hall of Fame partial save
Certain glitch Pokémon's sprites will corrupt existing Hall of Fame data when they are sent out or seen on the opponent's side, with the most well known being Missingno. and 'M (00). This is actually a partial save, but the player's main progress data is unchanged, so if the player resets the game after encountering a Missingno. their Hall of Fame data will be corrupted even if they do not save the game from the 'start menu'.
Not all glitch Pokémon do this, for example, the glitch Pokémon PkMn (F7) in Yellow, probably because it uses Bulbasaur sprite on both the opposing side and the user's side.