19. A computer-based system for generating comparison output files indicating non-matched annotations within files, the system comprising: a memory storing instructions; and a processor configured to execute the instructions to: identify first hidden characters for an insertion point and an end point of a first annotation in a first electronic file; identify a first portion of the first electronic file between the identified first hidden characters; identify second hidden characters for a second annotation in a second electronic file different than the first electronic file; identify a second portion of the second electronic file between the identified second hidden characters; generate an annotation index including the first portion and the second portion: compare the first portion with the second portion in the annotation index to determine whether the second annotation is a matching annotation corresponding to the first annotation; and generate, based on the comparison, a comparison output file including information for displaying a modified appearance of characters in the first annotation to indicate that the second electronic file does not contain a matching annotation.
19. A computer-based system for generating comparison output files indicating non-matched annotations within files, the system comprising: a memory storing instructions; and a processor configured to execute the instructions to: identify first hidden characters for an insertion point and an end point of a first annotation in a first electronic file; identify a first portion of the first electronic file between the identified first hidden characters; identify second hidden characters for a second annotation in a second electronic file different than the first electronic file; identify a second portion of the second electronic file between the identified second hidden characters; generate an annotation index including the first portion and the second portion: compare the first portion with the second portion in the annotation index to determine whether the second annotation is a matching annotation corresponding to the first annotation; and generate, based on the comparison, a comparison output file including information for displaying a modified appearance of characters in the first annotation to indicate that the second electronic file does not contain a matching annotation. 21. The computer-based system of claim 19 , wherein the second electronic file is a modified version of the first electronic file.