If this happens too often,  uncheck everything but "UI Prompt" in

Preferences/General/Security/Secure Storage/Master password providers

Then delete storage on Contents tab.

Atelier will create a master password and will ask you for it on every startup. This is annoying,  but sometimes better than having to recreate connections from scratch.

I've just reproduced the issue on "Cache for Windows (x86-64) 2017.2 (Build 671.0U QDTESTSYS) Tue May 9 2017 20:44:20 EDT"

POST http://192.168.2.178:57775/api/atelier/v1/SAMPLES/docs
Accept: application/json
Content-Type: application/json
["%Library.String.cls", "lookup1.mac"]
 -- response --
200 OK
Date:  Wed, 10 May 2017 12:57:58 GMT
Server:  Apache
Cache-Control:  no-cache
Expires:  Thu, 29 Oct 1998 17:04:19 GMT
Pragma:  no-cache
Transfer-Encoding:  chunked
Content-Encoding:  gzip
Keep-Alive:  timeout=120
Connection:  Keep-Alive
Content-Type:  application/json; charset=utf-8

{
    "status": {
        "errors": [],
        "summary": ""
    },
    "console": [],
    "result": {
        "content": [
            {
                "name": "%Library.String.cls",
                "db": "CACHELIB",
                "ts": "2017-05-09 20:31:58.000",
                "upd": true,
                "cat": "CLS",
                "status": "",
                "enc": false,
                "content": [
                    "IncludeGenerator %occUtility",
                    "",
                    "/// The %String data type class represents a string.",
                     ....
                ],                "console": []
            },
            {
                "name": "lookup1.mac",
                "db": "SAMPLES",
                "ts": "2002-01-03 12:07:15.000",
                "upd": true,
                "cat": "RTN",
                "status": "ОШИБКА #5001: Missing Source for Document: lookup1.MAC",
                "enc": false,
                "content": "",
                "console": []
            }
        ]
    }
}

Thank you for reporting, Atelier team will look into this.