Effects of Schengen Visa refusal appeal on new fresh visa

There is no cool-off period or mandatory delay between applications and a refusal does not imply a ban from the Schengen area so you could in principle reapply immediately and your new application should be evaluated on its own merits. Legally speaking, a pending appeal does not make that much of a difference either.

On the other hand, if your situation hasn't changed and you haven't done anything to address the concerns raised following your earlier application, your new application is likely to be rejected as well. Furthermore, all Schengen consulates will know about the previous refusal, from your passport but also from a database shared between Schengen countries. There is therefore no point in renewing your passport to disguise it or trying the same thing with different countries in the hope you might get lucky.

In your specific case, the details you have provided suggest that it was an extremely bad idea for you to reapply in the manner that you did. Until now, you only had one refusal, which is less than ideal but not that big a deal. But by reapplying immediately to another country and for another purpose, you run a high risk of damaging your credibility durably.

For it should be extremely hard for the Czech consulate to take your new application at face value, if they pay any attention at all. A few weeks ago, you claimed that you wanted to attend a conference in Spain. Now it appears you will not be working at all and in fact do not care so much about the conference but still want to go to the Schengen area during the exact same time period.

Similarly, adjusting the number of days you spend in this or that country to give you an opportunity to apply elsewhere gives the impression that you are trying to cheat. You can do that the first time around (don't tell them!) but not on a second application for the same trip because your objective is then transparent. Similarly a family or professional visit typically trumps tourism. If you want to attend a conference, it makes sense to assume that this is the real goal of your trip, even if you add a few days in the Czech Republic in an attempt to circumvent the rules.

Because of all this, it will hard to resist the conclusion that you are ready to make up any convenient story to obtain a visa and probably never intended to go to Spain either. This makes your current plan and anything you might say in the future very difficult to believe. It seems you realise that and hope cancelling the appeal would somehow help but the pending appeal really doesn't matter much now.