How do I mass flag a node on behalf of users (possibly with VBO)?
What you could do to get this to work, is to use the integration of VBO with the Rules module, as further detailed below.

Step 1: Create a Rules Component

Create a (rather basic) Rules component to flag a node by a user. Here is such component in Rules Export format:

{ "rules_flag_node_flagged_by_a_user" : {
    "LABEL" : "Flag node flagged by a user",
    "PLUGIN" : "rule",
    "OWNER" : "rules",
    "REQUIRES" : [ "flag", "rules" ],
    "USES VARIABLES" : {
      "flagging_user" : { "label" : "Flagging user", "type" : "user" },
      "flagged_node" : { "label" : "Node to be unflagged", "type" : "node" }
    },
    "DO" : [
      { "flag_flagnode" : {
          "flag" : "your_flag",
          "node" : [ "flagged-node" ],
          "flagging_user" : [ "flagging_user" ],
          "permission_check" : "1"
        }
      },
      { "drupal_message" : { "message" : "Node flagged for user  [flagging-user:name] (uid=[flagging-user:uid])" } }
    ]
  }
}


This Rules Component uses a flag with machine name your_flag. After you edit that machine name to fit the name of your flag, you should be able to import this rule in your own site (using the Rules UI, which needs to be enabled).

BTW: the Rules Action to display a message is just to see it at work while QA-testing this rule, feel free to remove that if you want.

Step 2: Let VBO do the work

This step is pretty easy ... Just use your VBO view. The clue to what you want VBO to do as an operation is ... Execute the Rules Component from Step 1.

If you're not familiar with how to do so, have a look at the video about Using Rules components with VBO". If you want even more, then also watch the subsequent "Using Rules components with more than one parameter" video.

Attention: to process like 100.000 records at once is quite a challenge (memory requirements, etc). Therefor you might want to also watch the video about "More details about VBO settings" ... Before you are tempted to use VBO for processing them all at once ...

Video tutorials

If you're not familiar (enough/yet) with Rules, checkout the 32 (!!!) great, and free, video tutorials Learn the Rules framework.

Happy VBO-ing while Rules-ing!

PS: I'm assuming this question is about D7.