Any image? I can't follow your questons?

https://www.dropbox.com/sh/a790tlv7oknna07/AADShNP4L2JqeZhx_y5aqHP5a?dl=0 In that folder you will find 3 PDF versions of my schematic prior to re-running Annotate (after I fixed it manually). I then ran annotate again, and the results are shown in the screenshots (I did not save these).

Annotate is suppose to sequentially label parts with the same prefix so they don't conflict. This fails not only because it mixes up packages U1 = Arduino Nano U2, U3 = SM2167 CD4066 is broken up into U1.4, U1.3, U3.2, U4.1 (???) Single LM358 (analog section) is U3.1 and U4.2 U1.1, U1.2 is a single LM358 (extractor page) U2.1, U2.2 is a single LM358 (extractor page0 U1 used for Nano and 2 parts of a CD4066 U2 is applied to a SM2167 and an LM358 U3 is assigned to a 2167 and one part of a CD4066 and 1/ an LM358 U4 is assigned to ¼ of a CD4066, ½ of an LM358 Is this making sense to you?

U1 also used for a LM358

A list of before and after part (reference designator) numbering would be most helpful. :)

You can see the before and after in my dropbox. Do you need me to list them out for you?

It saves time having to go to external sites if you can just post a text list here. It would be good if you could share you project either publicly or privately with Support. Thanks.

I would be glad to share it with support. How do I do that?

support@easyeda.com https://beta.easyeda.com/Doc/Tutorial/share.htm#Access-Control