You'll need to describe what you have in more detail. Modifying data in one table, will not modify data in another.
There are a few exceptions to that, however:
If you have a relationship between the two tables and you've enabled the "delete" option, deleting a record in one table can delete multiple related records in another.
If you have Lookups and/or calculaitons that refer to data in another table, modifying the data in one table might result in data in the other table changing.
You can also get the illusion that records are disappearing if a value used to define a relationship gets changed as this can "break" the relationship link. This is one way, for example, that records can seem to disappear out of a portal.