Baseline entries do not understand same resources in different directories

[jonny-graham-trade]

Describe the issue
Using Terraform to create AWS resources.
We have multiple copies of the same resource (e.g. in both dev and prod directories). When one of these is in the baseline file, the check skips for both.
This can give the impression that a vulnerability is resolved when it is actually being suppressed by a potentially unrelated file, as removing a file from the baseline doesn't cause it to fail the check.

Examples
Create two folders in your working root. Add a main.tf in both, containing:

data "aws_iam_policy_document" "route53_policy" {
  statement {
    effect = "Allow"
    actions = [
      "route53:ListHostedZones",
      "route53:GetHostedZone",
      "route53:ListTagsForResource"
    ]
    resources = ["*"]
  }
}

run checkov --directory . --create-baseline from the root.
This will add a failure for both files into the baseline (CKV_AWS_356)

Then, delete one of the files from the baseline.

checkov -d . --baseline .checkov.baseline
My expectation is that a scan should report the failure for the file that was removed from the baseline
Instead, both failures are still suppressed.

Version (please complete the following information):

• Tested both Checkov Version 3.2.495 and 3.2.513