Previous versions of your paper will remain publicly available. To allow authors to make changes to the comments and other meta-data fields without generating a new version, and hence date stamp, would effectively mean that all changes would be backdated to the time the last version was submitted. This is open to abuse and thus not allowed. The journal reference may contain only full publication information for the paper. Indicate the nature of the changes.
Readers like to know why a paper has been replaced.
Often, changes are of a minor nature, but if the author does not indicate this then readers will generally assume the worst. Therefore, you should give some reason for the replacement. If you do not, then the old comments will be lost. For instance, in the examples above, the TeX related comments and page counts were copied from the previous versions of the comments, since they are still valid and useful. Same day replacements do not generate a new version stamp.