Yes. If the filters/dashboards exist in the target and another one with the same name and owner is imported, the existing filter/dashboard will be overwritten with the configuration of the imported one. The owner is considered the same if it has the same username.
It does not matter if the users are not being transferred in this case. The key is whether the filters/dashboards can be considered the same as those existing in the target.
Currently you get a combination of both servers, as existing filters in target server will never be deleted, but they may be modified if they are imported from the source instance.
There is a feature request to disable modification of existing objects at PCP-404. Please vote it, if you find it interesting.
Just as an additional help, a table with the cases asked by Harish (I saw them in a notification email...) is available here.
The fact that users are not imported does not make any difference to the results described in that table. It could only make the creation of a new filter fail if its owner does not exist.
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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