Generally speaking, it is impossible to express the difference you intend just by changing verb form. 是, adjectives, and many other verbs are stative and they do not shift the reference time. We must either use particles like 了 or 过, or temporal adverbs like 以前 to set the reference time to the past.
Dynamic verbs are usually accompanied by particles and auxiliaries like 了, 会, etc, which normally put the time reference to the past or the future. Stative description usually complements dynamic one. I think this is generally true in many languages, so lacking tense is not particularly disturbing.
The only tricky case might be the counterfactual use of the past tense and when the verb is stative, as in your question. When you say I was working, you imply I am not working. In this case, adding contrastive adverbs like 以前, 从前, 本来, etc. can usually convey the same idea. If the adverbs do not work, you can always make the point clear explicitly by saying “，但现在不...了”. It is often common to add 现在 when asking questions like “你现在在哪工作”, “你现在住在哪” etc. even though 现在 is not absolutely necessary.
Some explanation of the dialogue: The question asks 不是... implying the speaker might have heard or learnt that somewhere. Because the speaker is trying to recall something from his memory, the listener replies 是的, which merely confirms the information source but does not assert about its availability in the present. She then explains that the situation has changed since then (when the observation was made) that it is not the case now. In this case, 不是的 is equally correct.
This usage might be more or less similar to English tense shifting. For example, she said she was working ... may well mean she is working ... as well as she is not working ...
Questions beginning with 不是 or 是不是 are often biased towards the positive answer. The speaker just want to the listener to confirm the information. If the information itself is imprecise, but not exactly false, the listener may well reply “是的” first and add an additional clarification. If the question is more neutral, e.g. “你在公司工作吗”, the purpose of asking this question is probably just to know the listener's current state. Although Chinese tense is always unmarked and the past tense interpretation is always an option, answering “在，但现在不在了” is not felicitous, unless in his opinion being working and having been working do not really matter much, or he intends to be amusing, like in “Could you help me?” “I could, but I don't want to.”
As far as I know, if the same question were asked in Japanese, both the past and present would be acceptable for a question about the present state, but the answer is usually either in the present or the past depending on the present fact because Japanese past tense generally assumes the opposite case in the present, too. But tense system does not exist in Chinese, so we do have the same assumption.
The last comment about 过: there is an odd contrast between 过 and 了. 了 often implies an immediate result of the verb is available, while 过 generally does not. So 门开了 sounds like the door is currently open, while 门开过 sounds like the door is not open, or at the very least the open state of the door is not the immediate result of the opening action the speaker refers to. The same difference apply to 水开了 and 水开过, 有人来了 and 有人来过. But the contrast is not consistent, for example, 吃过 and 吃了 mean pretty much the same thing. Although 了 and 过 can be used with stative verbs, they cannot be used with 是 and 在, which may be due to their special grammatical functions.