Yes and No. If you were using the native "fixVersion" field in Jira to track this data, then Yes. You can use historical operators such as WAS on that specific field in order to find out if an issue previously had a specific value on that field. The Advanced Searching Fields Reference explains this is possible. And example JQL could be something like:
fixVersion WAS "Version 1.0"
However if you were using a custom field of type version, or a custom text field to store this data, unfortunately the answer appears to be No. These other fields do not appear to currently be able to track those kinds of historical changes.
There is a feature request to add the ability in Jira to track this kind of information for all fields in https://jira.atlassian.com/browse/JRASERVER-30663
From reading the comments on that feature request, it looks like there might be a plugin for Jira called the SQL for Jira Driver: Convert JQL to SQL, this plugin appears to allow you to search for historical issue data in a SQL format. I realize that might not be ideal for what you are looking for here, but I don't believe that Jira will be able to natively search through JQL for these kinds of custom fields for this information at this time.
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