Ok, if you appeal and then submit a new application then the new application must disclose that you have an appeal pending. This is likely to result in you being asked if you want to proceed with the application or the appeal - you would be expected to choose one. Therefore you should not usually submit a new application if you have an appeal pending.
There are exceptional circumstances where an applicant might let an appeal go for a while before submitting a new application - the intent would be to buy time and then change to the new application, but BOTH should not be considered at the same time. This is why I am not saying you cannot submit an application while an appeal is pending but I am telling you what will happen if you do this.
If you make the application then it might be accepted in terms of taking your payment but you will usually then be asked to choose the appeal or the application. The general advice is therefore to NOT submit an application while the appeal is pending UNLESS you have a specific reason for wanting to submit a different application that will replace the appeal.
If your refusal was very recent then you can quickly submit a new application because your leave to remain will have effectively been extended pending receipt of the decision and your leave will therefore effectively have ended on the date of the decision. You are of course allowed to submit a new application up to 28 days after your leave to remain expires. A new application should therefore be accepted.
I hope that is clear.
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