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.

Thank you for reporting.

This is a known issue that is planned to be fixed in Atelier 1.1. (May be available earlier in beta)

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"

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.

Thanks! This seems like a new defect, so your report will help us fix it.
Could you please also check what's Problem view shows when you see project error marker after all errors are fixed (as per your second reported defect)?
Also, are there any errors in Error Log view (Window/Show view/Other/General/Error Log)?

Could you please check "Problems" view to see if it has a description for the error marker?