When I edit a project, and save multiple times, and close the program To come back to a project later. Then when I reopen and try to edit the same project, some of the segments are either missing, or out of alignment.
If you are just saving with the same file name, then whatever was saved last is all there is. The program never comes back with an earlier version of what was saved, unless you use one of the back up files, like one that finishes with _BAK2.MV_, where 2 goes from 0 to 9. What you are describing is something else, like forgetting to save before exiting, or crashing before saving. When you close the program, if you have not saved the latest changes, then you are prompted to save. If you do not save, then your changes are not saved.
Just a guess here but if you need multiple backups of a project at various stages, use the 'Save As' option and give them different labels such as (project name) V1, V2, etc.
As John said, otherwise you have only the last version of the project saved unless you use a BAK file which is not always visible within MEP and may not be the one you need as they are set to time intervals.