When using a program to encrypt a file, compare the file's final size with its original size in bytes (not KiB or grosser), and allow for the standard difference required by the particular encryption method used. Otherwise, you'll have lost your stuff.
I don't want to identify the third-party program or cipher I use (the program isn't the latest, anyway). Suffice it to point out that it sometimes reports successful encryption but has yielded a much smaller file than the original. Encryption is not compression; unless compression is inherent in the cipher you use, the size should be exactly the same, as measured in bytes, except for additional bytes needed for overhead required by the particular encryption method used, such as bytes that identify the cipher used and store a key or password hash. You may have to create test files to find out the length overhead for a given password and set of parameters; verify the test file decrypts properly.
Decrypt the file as a test because a bad-length file likely won't decrypt intelligibly. Test using a file the contents of which will be familiar to you.
Do not encrypt so as to overwrite your only instance of the plaintext file or a bad encryption will leave you without anything. Either encrypt a copy if you overwrite, so the original will still be intact elsewhere, or don't overwrite your only instance, i.e., write elsewhere. Which is more secure (against an attacker reading pre-encryption file fragments left behind) depends on your setup.