OP, you have identified your source as Josephus's passage where he says:
But when God came into the garden, Adam, who was wont before to come and converse with him, being conscious of his wicked behaviour, went out of the way. This behaviour surprised God; and he asked what was the cause of this his procedure; and why he, that before delighted in that conversation, did now fly from it, and avoid it?
and are looking for a rabbinic "source." But our rabbinic sources--especially aggadic midrashim--were redacted well after Josephus wrote his works at the end of the 1st century CE. At best, you might find rabbinic sources reflecting the same tradition or idea. But Josephus also often records stories and detail we do not have other sources for, perhaps because they reflect lost traditions or because they are non-canonical "street Torah."
However, many of these elements are found in at least some rabbinic sources. In Bereshit Rabbah 19:9, Hashem laments the fall of man. The text links the word "ayeka" (where are you) to "eikh heveit" (roughly, what has happened to you!) and to "eicha" (the first word of Lamentations, which has the same implication of sad shock: how [has it happened]). In elaborating, the midrash says God was commenting on both the fact that man has become disgraced and that man has become distant from Hashem. The key phrase I'm thinking of is: אֶתְמוֹל לְדַעְתִּי, וְעַכְשָׁיו לְדַעְתּוֹ שֶׁל נָחָשׁ - roughly, yesterday Adam was was in accord with me, today he is in accord with the Serpent.
The Etz Yosef explains:
אתמול לדעתי התבונן איך נפלת ממדרגתך. כי בתחלה לא היה בך כח הרע מאומה ונמשכת לדעתי ורצוני. והיום לדעתו וחפצו של נחש לכח הרע ואתמול הכוונה כמו קודם ותחלה: Translation: God is reflecting on how much you have fallen. At first, there was no evil in you and you sought to know me and do my will. Today, you do what the Serpent wants for evil...
Bereshit Rabbah 21:4 has a similar statement and the Etz Yosef makes a similar comment.
In Sanhedrin 38b we find: ואמר רב יהודה אמר רב אדם הראשון מין היה שנאמר ויקרא ה' אלהים אל האדם ויאמר לו איכה אן נטה לבך. Rav Yehudah said in the name of Rav, Adam was a heretic. Because the verse says God called out to man and said "where are you" (ayeka), meaning where has your heart turned to.
As for the element of surprise that man has turned away and hidden, Sforno to 3:9 comments that "ayeka" is not a question of where man is but is asking (or observing) "that you do not appear in the garden as you used to, because now you are hiding and you did not do that before."
So, putting these sources together, we have most of the elements of your OP and the Josephus passage: God is surprised that man is hiding from him which is not what he used to do (Sforno); God is disappointed about the fall of man (Bereshit Rabbah); and God laments that that man used to want be be close to Him and/or listen to Him but has now gone in a different direction (Bereishit Rabbah & Sanhedrin). The only elements I'm not seeing are (a) anthropomorphizing that God misses Adam (which I don't see in the Josephus quote either) and (b) the specific idea that Adam used to "delight" in talking to God.