Colors Reverting on Conditional Formated Chart

I've been struggling with an issue for several weeks and I really hope someone on this forum can help me out. I've created an automated tracking tool that I uses excel to create a dynamically updating bar chart tracking hold times for activities. Basically the bar gets bigger as a given activity is on hold, and then the colors change to yellow and then red if they are on hold too long. The problem I am having is that if we clear our entire queue of work, then when we enter a new work item a few minutes or hours later, the color scheme for the bars revert back to what I assume is an excel default. Since we are using this tool as a visual workplace tracker, the color scheme is important and I cannot for the life of me figure out how to prevent excel from changing the color.

There are a few macros running to the generate a realtime clock and to automatically reapply the autofilter to add/remove work items as they come and go. The color scheme change is controlled using a conditional formatting table. Everything works perfectly, except the issue where the colors I select for the conditional formatted columns keep changing. Thanks in advance to anyone who can offer some advice on my conundrum.

Thanks for the welcome and sorry for not being clear enough with my description. I'll break down the workflow for the by steps.

1) New work item comes in and team logs it into the tool based on date/time, and then selects back to the worksheet tab showing the chart
2) The new work item is added automatically as another bar to the chart (starts as purple) and the bar starts growing over time as the work item is in progress
3) If the work time exceeds the "warning" time, the bar turns yellow and if it goes past the limit time it will turn red
4) Once the work is complete, the team member enters current time/date and then the chart automatically removes the bar and resizes any remaining bars still in queue

The issue occurs when we happen to clear all of the work items out of the queue and basically have a blank chart. When the next item comes in and is added to the tool, the color scheme is changed which ruins some of the key functionality. I hope that clarifies a bit better what is occurring. Thank you again for all the help

That is an interesting idea. I'll give it a shot and reply with my results. Thanks!